From 49bc606b8e20c71e5529050a8d01df77a5614c4c Mon Sep 17 00:00:00 2001 From: Anh Nguyet Vu Date: Wed, 20 Oct 2021 15:34:42 -0600 Subject: [PATCH] Add terms and modify template to support PDX annotation --- NF.csv | 622 +++++++++++++++++++++++++++++++ NF.jsonld | 1044 +++++++++++++++++++++++++++++++++++++++++------------ 2 files changed, 1434 insertions(+), 232 deletions(-) create mode 100644 NF.csv diff --git a/NF.csv b/NF.csv new file mode 100644 index 00000000..36e8fea2 --- /dev/null +++ b/NF.csv @@ -0,0 +1,622 @@ +Attribute,Description,Valid Values,DependsOn,Required,Source,Parent,Properties,DependsOn Component,Validation Rules +channel,Fluorescent color labeling for an array,"Cy5, Cy3",,TRUE,,array,,, +photograph,An image recorded by a camera.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C86035,assay,,, +HPLC,"Frequently referred to simply as HPLC, this form of column chromatography is used frequently in biochemistry. The analyte is forced through a column by liquid at high pressure, which decreases the time the separated components remain on the stationary phase.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C16434,assay,,, +elevated plus maze test,"A method which utilizes an experimental apparatus consisting of four arms, usually two enclosed and two open, in the shape of a plus (+) upon which the test animal can walk. The maze is elevated a set distance, for example 40 to 60 centimeters, above the floor or platform upon which the apparatus sits.",,,FALSE,http://purl.obolibrary.org/obo/MMO_0000262,assay,,, +open field test,"A test utilizing an enclosure consisting of a single area bordered by clear or opaque walls, used to measure movement, exploratory behavior, etc of an experimental subject.",,,FALSE,http://purl.obolibrary.org/obo/MMO_0000258,assay,,, +rotarod performance test,"A method that utilizes a device consisting of a rotating rod the speed of which is mechanically driven and precisely controlled, for instance held constant or accelerated. The rotarod test is often used to measure riding time or endurance in order to evaluate balance, motor coordination or grip strength.",,,FALSE,http://purl.obolibrary.org/obo/MMO_0000567,assay,,, +mRNAcounts,A mRNA profiling assay using digital molecular barcoding technology to quantify target mRNA molecules without the need for amplification.,,,FALSE,Sage Bionetworks,assay,,, +high content screen,An image analysis technique combining automated fluorescence microscopy with multi-parameter quantitative image analysis for the large scale study of cells (cellomics).,,,FALSE,http://www.ebi.ac.uk/efo/EFO_0007550,assay,,, +Immunocytochemistry,The branch of immunochemistry dealing with cells and cellular activity; the application of immunochemical techniques to cytochemistry.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C17731,assay,,, +immunofluorescence,An immunological procedure in which the antibodies are coupled with molecules which fluoresce under ultra violet (UV) light. This makes them particularly suitable for detection of specific antigens in tissues or on cells.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C17370,assay,,, +autoradiography,A radioactivity detection technique using X- ray film to visualize molecules or fragments of molecules that have been radioactively labeled.,,,FALSE,http://purl.obolibrary.org/obo/ERO_0000716,assay,,, +reporter gene assay,"Reporter gene assay measures the gene expression from a reporter gene. The reporter gene is inserted under the control of a foreign promoter or an artificial regulatory element of interest. Reporters include luciferase, beta galactosidase, beta lactamase, chloramphenicol acetyl transferase, or a fluorescent protein.",,,FALSE,http://purl.obolibrary.org/obo/OBI_0002082,assay,,, +electrochemiluminescence,"A method in which electromagnetic radiation, in the form of light emission, is generated from an electrochemical reaction in a solution.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C111193,assay,,, +Real Time PCR,An application of PCR that measures the products generated during each cycle of the polymerase chain reaction process in order to determine the starting amount of template in the reaction.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C51962,assay,,, +in vivo tumor growth,"The growth of a tumor measured using calipers, ruler, or another similar measurement device. See also ""in vivo bioluminescence"".",,,FALSE,Sage Bionetworks,assay,,, +scale,An instrument or machine for weighing.,,,FALSE,http://purl.obolibrary.org/obo/MMO_0000217,assay,,, +Blood Chemistry Measurement,The determination of the measured concentrations of chemical constituents of the blood by assay in a clinical laboratory.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C47868,assay,,, +in vivo bioluminescence,An imaging assay that allows detection of bioluminescence from a living organism or organisms.,,,FALSE,http://purl.obolibrary.org/obo/ERO_0000651,assay,,, +immunohistochemistry,An immunostaining assay to detect and potentially localize antigens within the cells of a tissue section,,,FALSE,http://purl.obolibrary.org/obo/OBI_0001986,assay,,, +NOMe-Seq,Nucleosome Occupancy and Methylome Sequencing,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C106053,assay,,, +FIA-MSMS,Flow injection analysis - tandem mass spectrometer,,,FALSE,https://www.ncbi.nlm.nih.gov/pubmed/28667829,assay,,, +UPLC-MSMS,Ultra performance liquid chromatography - tandem mass spectrometer.,,,FALSE,https://www.wur.nl/en/show/Ultra-performance-liquid-chromatography-tandem-mass-spectrometer-UPLCMSMS.htm,assay,,, +HPLC-MSMS,"An analytical technique wherein high performance liquid chromatography is coupled to tandem mass spectrometry in order to separate, identify, and quantify substances in a sample.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C120691,assay,,, +liquid chromatography-electrochemical detection,"A liquid chromatography method that is sensitive to compounds which can be either reduced or oxidised. The mobile phase passes directly over the working electrode, which is set to the specific potential required for oxidation or reduction. The current produced is then measured.",,,FALSE,http://purl.obolibrary.org/obo/CHMO_0001746,assay,,, +rnaSeq,RNA Sequencing measurements,,,FALSE,http://purl.obolibrary.org/obo/OBI_0001271,assay,,, +mirnaSeq,Small RNA measurements collected from RNA-Seq experiments,,,FALSE,http://purl.obolibrary.org/obo/OBI_0002112,assay,,, +LC-MSMS,A method where a sample mixture is first separated by liquid chromatography before being ionised and characterised by mass-to-charge ratio and relative abundance using two mass spectrometers in series,,,FALSE,http://purl.obolibrary.org/obo/CHMO_0000701,assay,,, +LC-MS,A method where a sample mixture is first separated by liquid chromatography before being converted into ions which are characterised by their mass-to-charge ratio and relative abundance,,,FALSE,http://purl.obolibrary.org/obo/CHMO_0000524,assay,,, +lncrnaSeq,Long non-coding RNA measurements collected from RNA-Seq experiments,,,FALSE,,assay,,, +Whole Exome Sequencing,A procedure that can determine the DNA sequence for all of the exons in an individual. ,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C101295,assay,,, +Sanger sequencing,"A DNA sequencing technique in which a mixture of deoxynucleosidetriphosphates (dNTPs) and chain-terminating dNTPs, which are radioactively or fluorescently labeled, are combined within the reaction mixture. Once the reaction is complete, the DNA strands are separated by size, and the labeled chain terminating dNTPs can be read in sequence by the investigator or by a machine.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C19641,assay,,, +ChIPSeq,Chromatin immuno-precipitation followed by sequencing,,,FALSE,http://purl.obolibrary.org/obo/OBI_0000716,assay,,, +rnaArray,RNA measurements captured by array technology,,,FALSE,http://purl.obolibrary.org/obo/OBI_0001463,assay,,, +snpArray,SNP measurements captured by array technology,,,FALSE,http://purl.obolibrary.org/obo/OBI_0001204,assay,,, +methylationArray,Methylation data captured by array technology,,,FALSE,http://purl.obolibrary.org/obo/OBI_0001332,assay,,, +mirnaArray,microRNA measurements captured by array technology,,,FALSE,http://purl.obolibrary.org/obo/OBI_0001335,assay,,, +bisulfiteSeq,Methylation data captured by sequencing of DNA treated by a bisulfite-based chemical process,,,FALSE,http://purl.obolibrary.org/obo/OBI_0000748,assay,,, +ATACSeq,Open chromatin regions measured by sequencing DNA after assay for transposase-accessible chromatin (ATAC) treatment,,,FALSE,http://purl.obolibrary.org/obo/OBI_0002039,assay,,, +HI-C,Chromatin interactions detected by HI-C protocol,,,FALSE,http://www.ebi.ac.uk/efo/EFO_0007693,assay,,, +errBisulfiteSeq,Data for enriched reduced representation bisulfite sequencing data,,,FALSE,,assay,,, +ISOSeq,Full isoform sequencing,,,FALSE,,assay,,, +westernBlot,A multistep process in which a mixture of proteins is separated by gel electrophoresis,,,FALSE,http://purl.obolibrary.org/obo/MMO_0000338,assay,,, +wholeGenomeSeq,Laboratory technique to sequence the complete DNA sequence of an organism's genome at a single time,,,FALSE,http://edamontology.org/topic_3673,assay,,, +polymeraseChainReaction,"A rapid technique for in vitro amplification of specific DNA or RNA sequences, allowing small quantities of short sequences to be analyzed without cloning",,,FALSE,http://purl.obolibrary.org/obo/MMO_0000459,assay,,, +cellViabilityAssay,This assay type measures the cellular state of living or dying by measuring an indicator of life or death,,,FALSE,http://www.bioassayontology.org/bao#BAO_0003009,assay,,, +atomicForceMicroscopy,Microscopy which uses a sharp spike (known as a 'tip') mounted on the end of a cantilever to scan the surface of the specimen,,,FALSE,http://purl.obolibrary.org/obo/CHMO_0000113,assay,,, +brightfieldMicroscopy,Microscopy where the specimen is illuminated with light transmitted from a source on the opposite side of the specimen from the objective,,,FALSE,http://purl.obolibrary.org/obo/CHMO_0000104,assay,,, +tractionForceMicroscopy,An experimental method for determining the tractions on the surface of a biological cell by obtaining measurements of the surrounding displacement field within an in vitro extracellular matrix (ECM),,,FALSE,https://en.wikipedia.org/wiki/Traction_force_microscopy,assay,,, +Phase-Contrast Microscopy,A simple non-quantitative form of interference microscopy of great utility in visualising live cells. Small differences in optical path length due to differences in refractive index and thickness of structures are visualised as differences in light intensity.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C16857,assay,,, +nextGenerationTargetedSequencing,A type of next generation sequencing in which specific genes or portions of genes are targeted for sequencing using amplicon-based workflow.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C130177,assay,,, +jumpingLibrary,,,,FALSE,,assay,,, +MIB/MS,Kinomics assay using multiplexed kinase inhibitor beads and mass spectrometry (MIB/MS),,,FALSE,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3328787/,assay,,, +scCGIseq,"A method for genome-wide CpG island (CGI) methylation sequencing for single cells (scCGI-seq), combining methylation-sensitive restriction enzyme digestion and multiple displacement amplification for selective detection of methylated CGIs",,,FALSE,https://www.ncbi.nlm.nih.gov/pubmed/28126923,assay,,, +MudPIT,MudPIT is a method for rapid and large-scale protein identification by multidimensional liquid chromatography associated with tandem mass spectrometry,,,FALSE,http://purl.obolibrary.org/obo/MI_0658,assay,,, +questionnaire,"A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study.",,,FALSE,http://purl.obolibrary.org/obo/OBI_0001000,assay,,, +DNA optical mapping,Fluorescent imaging of linearly extended DNA molecules to probe information patterns along the molecules,,,FALSE,https://doi.org/10.1016/j.copbio.2013.01.009,assay,,, +oxBS-Seq,Oxidative bisulfite sequencing (oxBS-Seq) to map 5-methylcytosine and 5-hydroxymethylcytosine,,,FALSE,http://www.ebi.ac.uk/efo/EFO_0008840,assay,,, +Ribo-Seq,Ribosome profiling (Ribo-Seq).,,,FALSE,http://www.ebi.ac.uk/efo/EFO_0008891,assay,,, +Positron Emission Tomography,A technique for measuring the gamma radiation produced by collisions of electrons and positrons (anti-electrons) within living tissue.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C17007,assay,,, +RPPA,Reverse phase protein array (RPPA) is a an assay that measures multiple protein expression levels in a large number of biological samples simultaneously using high quality antibodies,,,FALSE,http://www.bioassayontology.org/bao#BAO_0010030,assay,,, +ELISA,"A highly sensitive technique for detecting and measuring antigens or antibodies in a solution; the solution is run over a surface to which immobilized antibodies specific to the substance have been attached, and if the substance is present, it will bind to the antibody layer, and its presence is verified and visualized with an application of antibodies that have been tagged in some way.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C16553,assay,,, +LTP,Any measurable or observable characteristic related to the persistent robust synaptic response induced by synchronous stimulation of pre- and postsynaptic cells.,,,FALSE,http://purl.obolibrary.org/obo/VT_0002207,assay,,, +LFP,An extracellular electrophysiology assay where a microelectrode is placed in the extracellular space of brain tissue to measure action potential and compared to an electrode either outside or inside that tissue.,,,FALSE,http://purl.obolibrary.org/obo/OBI_0002189,assay,,, +whole-cell patch clamp,"A patch-clamp assay where the electrode is left in place on the cell, as in cell-attached recordings, but the membrane patch has been perforated, providing access from the interior of the pipette to the intracellular space of the cell. Measurements made with this technique involve recording currents through multiple channels simultaneously, over the membrane of the entire cell.",,,FALSE,http://purl.obolibrary.org/obo/OBI_0002178,assay,,, +sandwich ELISA,"The sandwich ELISA measures the amount of antigen between two layers of antibodies. The antigens to be measured must contain at least two antigenic sites, capable of binding to antibody, since at least two antibodies act in the sandwich. So sandwich assays are restricted to the quantitation of multivalent antigens such as proteins or polysaccharides. Sandwich ELISAs for quantitation of antigens are especially valuable when the concentration of antigens is low and/or they are contained in high concentrations of contaminating protein.",,,FALSE,https://www.ebi.ac.uk/ols/ontologies/bao/terms?iri=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23BAO_0002421,assay,,, +Laser Speckle Imaging,"A noninvasive, non-scanning optical imaging technique that provides full-field visualization of blood flow to the tissue being imaged, which provides information about tissue perfusion and the efficiency of disease treatment.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C116492,assay,,, +Genotyping,The determination of the DNA sequence of an individual.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C45447,assay,,, +TMT quantitation,"An isobaric labeling technique that uses tags containing four regions with the same total molecular weights and structure, so that during chromatographic or electrophoretic separation and in single MS mode, molecules labelled with different tags are indistinguishable.",,,FALSE,http://purl.obolibrary.org/obo/ERO_0002175,assay,,, +label free mass spectrometry,"A mass spectrometry assay that allows for measurement for endogenous targets in live cell assays, and eliminates the need for tags, dyes, or specialized reagents or engineered cells.",,,FALSE,http://purl.obolibrary.org/obo/ERO_0000708,assay,,, +cell count,A procedure to determine the number of cells in a sample. Also used to mean the result of such a procedure. ,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C48938,assay,,, +immunoAssay,Generic immunology assay,,immunoAssayType,FALSE,,assay,,, +Conventional MRI,"Magnetic resonance imaging using standard protocols for high resolution structural and anatomic characterization, including T1 weighted, T2 weighted, fluid attenuated inversion recovery (FLAIR), and gadolinium-enhanced sequences. [ NCI ]",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C175525,assay,,, +Functional MRI,The principle of functional MRI imaging is to take a series of images of an organ in quick succession and to statistically analyze the images for differences among them. Most commonly used in studies of brain function. [ NCI ],,,FALSE,http://purl.obolibrary.org/obo/NCIT_C17958,assay,,, +Magnetic Resonance Spectroscopy,Detection and measurement of the resonant spectra of molecular species in a tissue or sample.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C16810,assay,,, +MRISequence,The scanning sequence/modality that is used for a conventional MRI scan. ,"T1-weighted,T2-weighted,PD-weighted,Short Tau Inversion Recovery",,FALSE,Sage Bionetworks,experimentalData,,, +T1-weighted,,,,FALSE,Sage Bionetworks,MRISequence,,, +T2-weighted,,,,FALSE,Sage Bionetworks,MRISequence,,, +PD-weighted,,,,FALSE,Sage Bionetworks,MRISequence,,, +Short Tau Inversion Recovery,,,,FALSE,Sage Bionetworks,MRISequence,,, +head,The head is the anterior-most division of the body.,,,FALSE,http://purl.obolibrary.org/obo/UBERON_0000033,bodyPart,,, +transplantationType,"Type of transplantation involved in the experiment, derived from MESH","allograft, xenograft, autograft, isograft",,FALSE,,cancer,,, +transplantationRecipientSpecies,Species into which donor tissue was grown,"Human, Mouse",,FALSE,,cancer,,, +tumorType,The type of tumor that the biospecimen used to generate the data were collected from. ,"Cutaneous Neurofibroma, Plexiform Neurofibroma, Atypical Neurofibroma, Malignant Peripheral Nerve Sheath Tumor, Adenocarcinoma, Carcinoma, Ductal Carcinoma, Melanoma, Glioma, Low Grade Glioma, Diffuse Astrocytoma, Anaplastic Astrocytoma, Glioblastoma, Schwannoma, Lymphoblastic Lymphoma, Meningioma, Myeloma, normal, T Acute Lymphoblastic Leukemia, chronic lymphocytic leukemia, Acute Myeloid Leukemia, teratoma, Massive Soft Tissue Neurofibroma, Diffuse Infiltrating Neurofibroma, Localized Neurofibroma, Neurofibroma, Neurofibroma with Degenerative Atypia",,FALSE,Sage Bionetworks [RJA],cancer,,, +genePerturbationType,Specific way in which a single gene was perturbed in a sample,"overexpression, knockdown, knockout, Not Applicable",genePerturbationTechnology,FALSE,,cancer,,, +genePerturbationTechnology,Technology used to perform gene perturbation,"RNAi, CRISPR, CRE Recombinase",,FALSE,,cancer,,, +timePointUnit,For timed experiments this represents the unit of time measured,"seconds, minutes, hours, days, weeks, months",,FALSE,,cancer,,, +Schwann cell precusor,A giioblast cell that develops from a migratory neural crest cell. The SCP is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has no basal lamina. In rodents SCPs are the only cells in the Schwann cell linage that expresses Cdh19.,,,FALSE,http://purl.obolibrary.org/obo/CL_0002375,cellType,,, +B-lymphocytes,A lymphocyte of B lineage with the phenotype CD19-positive and surface immunoglobulin-positive.,,,FALSE,https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000236,cellType,,, +Embryonic stem cells,Embryonic stem (ES) cells are cells derived from the inner cell mass of the early embryo that can be propagated indefinitely in the primitive undifferentiated state while remaining pluripotent.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C12935,cellType,,, +iPSC,Induced pluripotent stem cells (iPS cells or iPSCs) are a type of pluripotent stem cell artificially derived from a non-pluripotent cell.,,,FALSE,https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0004905,cellType,,, +iPSC-derived telencephalic organoids,three-dimensional neural cultures (organoids) derived from induced pluripotent stem cells.,,,FALSE,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4519016/,cellType,,, +GABAergic neurons,A neuron that uses GABA as a vesicular neurotransmitter.,,,FALSE,https://www.ebi.ac.uk/ols/ontologies/zfa/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FZFA_0009276,cellType,,, +monocytes,"Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells.",,,FALSE,https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000576,cellType,,, +microglia,"The small, non-neural, interstitial cells of mesodermal origin that form part of the supporting structure of the central nervous system.",,,FALSE,https://www.ebi.ac.uk/ols/ontologies/bto/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBTO_0000078,cellType,,, +macrophages,"A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells.",,,FALSE,https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000235,cellType,,, +astrocytes,"Astrocytes (from 'star' cells) are irregularly shaped with many long processes, including those with end-feet which form the glial (limiting) membrane and directly and indirectly contribute to the blood-brain barrier.",,,FALSE,https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000127,cellType,,, +SH-SY5Y,Human neuroblastoma clonal subline of the neuroepithelioma cell line SK-N-SH that had been established in 1970 from the bone marrow biopsy of a 4-year-old girl with metastatic neuroblastoma.,,,FALSE,https://www.ebi.ac.uk/ols/ontologies/bto/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBTO_0000793,cellType,,, +GLUtamatergic neurons,"Have Glutamate receptors, which are synaptic receptors located primarily on the membranes of neuronal cells. Glutamate (the conjugate base of glutamic acid) is abundant in the human body, but particularly in the nervous system and especially prominent in the human brain.",,,FALSE,https://en.wikipedia.org/wiki/Glutamate_receptor,cellType,,, +NeuN+,Is a neuronal nuclear antigen that is commonly used as a biomarker for neurons and NeuN immunoreactivity has been widely used to identify neurons in tissue culture to measure the neuron(positive)/glia(negative) ratio in brain regions.,,,FALSE,https://en.wikipedia.org/wiki/NeuN,cellType,,, +NeuN-,Is a neuronal nuclear antigen that is commonly used as a biomarker for neurons and NeuN immunoreactivity has been widely used to identify neurons in tissue culture to measure the neuron(positive)/glia(negative) ratio in brain regions.,,,FALSE,https://en.wikipedia.org/wiki/NeuN,cellType,,, +epithelial,Somatic cells that cover the surface of the body and line its cavities.,,,FALSE,https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000066,cellType,,, +epithelial-like,"In cell morphology, epithelial-like cells are polygonal in shape with more regular dimensions, and grow attached to a substrate in discrete patches.",,,FALSE,https://www.thermofisher.com/us/en/home/references/gibco-cell-culture-basics/cell-morphology.html,cellType,,, +fibroblast,A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped.,,,FALSE,https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000057,cellType,,, +round,A phenotype observation at the level of the cell shape where the cell is round,,,FALSE,https://www.ebi.ac.uk/ols/ontologies/cmpo/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fcmpo%2FCMPO_0000118,cellType,,, +lymphoblast,"Often referred to as a blast cell. Unlike other usages of the suffix -blast a lymphoblast is a further differentiation of a lymphocyte, T- or B-, occasioned by an antigenic stimulus. The lymphoblast usually develops by enlargement of a lymphocyte, active re-entry to the S phase of the cell cycle, mitogenesis and production of much m-RNA and ribosomes.",,,FALSE,https://www.ebi.ac.uk/ols/ontologies/bto/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBTO_0000772,cellType,,, +polygonal,"A polygonal face is a polygon bounded by a circuit of polygon edges, and includes the flat (plane) region inside the boundary.",,,FALSE,https://www.ebi.ac.uk/ols/ontologies/sio/terms?iri=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_000503,cellType,,, +CD8+ T-Cells,"Is a T lymphocyte (a type of white blood cell) that kills cancer cells, cells that are infected (particularly with viruses), or cells that are damaged in other ways.",,,FALSE,https://en.wikipedia.org/wiki/Cytotoxic_T_cell,cellType,,, +arachnoid,An arachnoid mater is a delicate membrane that encloses the spinal cord and brain and lies between the pia mater and dura mater.,,,FALSE,https://www.ebi.ac.uk/ols/ontologies/bto/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBTO_0001636,cellType,,, +meningioma,A central nervous system cancer tissue that are manifested in the central nervous system and arise from the arachnoid 'cap' cells of the arachnoid villi in the meninges.,,,FALSE,https://www.ebi.ac.uk/ols/ontologies/doid/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_3565,cellType,,, +schwannoma,"A neoplasm that arises from SCHWANN CELLS of the cranial, peripheral, and autonomic nerves.",,,FALSE,https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0000693,cellType,,, +oligodendrocyte,A class of large neuroglial (macroglial) cells in the central nervous system. Form the insulating myelin sheath of axons in the central nervous system.,,,FALSE,http://purl.obolibrary.org/obo/CL_0000128,cellType,,, +schwann,Schwann cells are a variety of glial cell that keep peripheral nerve fibres (both myelinated and unmyelinated) alive.,,,FALSE,https://www.ebi.ac.uk/ols/ontologies/bto/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBTO_0001220,cellType,,, +iPSC-derived neuron,,,,FALSE,Sage Bionetworks,cellType,,, +iPSC-derived glia,,,,FALSE,Sage Bionetworks,cellType,,, +iPSC-derived astrocytes,,,,FALSE,Sage Bionetworks,cellType,,, +monocyte-derived microglia,,,,FALSE,Sage Bionetworks,cellType,,, +iPSC-derived neuronal progenitor cell,,,,FALSE,Sage Bionetworks,cellType,,, +CD138+,,,,FALSE,,cellType,,, +CNON,Cultured Neuronal cells derived from Olfactory Neuroepithelium,,,FALSE,https://www.synapse.org/#!Synapse:syn4590897,cellType,,, +teratoma,"A non-seminomatous germ cell tumor characterized by the presence of various tissues which correspond to the different germinal layers (endoderm, mesoderm, and ectoderm). It occurs in the testis, ovary, and extragonadal sites including central nervous system, mediastinum, lung, and stomach",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C3403,cellType,,, +Cy5,Fluorescent dye used for the red channel on an array,,,FALSE,http://purl.obolibrary.org/obo/FBbi_00000450,channel,,, +Cy3,Fluorescent dye used for the green channel on an array,,,FALSE,http://purl.obolibrary.org/obo/FBbi_00000449,channel,,, +drugScreenType,String describing general class of drug screen,"singleMolecule, smallMoleculeLibraryScreen, combinationLibraryScreen, combinationScreen",,FALSE,,compoundScreen,,, +curatedDataType,The type of information being curated.,"reference sequence, gene symbol, clinical data, gene function, chemical descriptor",,TRUE,,curatedData,,, +referenceSet,"A set of references (e.g., canonical assembled contigs) which defines a common coordinate space for comparing reference-aligned experimental data.","GRCh38, GRCh37, MMUL1.0, HRC",,TRUE,,curatedData,,, +reference sequence,Syntactic sequences that has a role as reference of an annotation.,,,FALSE,http://rdf.biosemantics.org/ontologies/rsa#ReferenceSequence,curatedDataType,,, +gene symbol,A unique gene name approved by an organism specific nomenclature committee.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C43568,curatedDataType,,, +clinical data,Data obtained through patient examination or treatment.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C15783,curatedDataType,,, +gene function,A term that expresses the function of a gene product.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C48933,curatedDataType,,, +chemical descriptor,"A chemical descriptor is a data item (quantity or value) about a chemical entity that conforms to a specification for how it is calculated, measured or recorded.",,,FALSE,http://semanticscience.org/resource/CHEMINF_000123,curatedDataType,,, +normalized,A data set that is produced as the output of a normalization data transformation.,,,FALSE,http://purl.obolibrary.org/obo/OBI_0000451,dataSubtype,,, +dataMatrix,A file of data containing multiple values for multiple samples.,,,FALSE,,dataSubtype,,, +raw,"A data file produced by an instrument, or one with very little subsequent processing.",,,FALSE,,dataSubtype,,, +processed,A file of data generated from running one or more bioinformatics methods on a raw file.,,,FALSE,,dataSubtype,,, +metadata,"A file of clinical, technical, or other parameters that describe a dataset.",,,FALSE,,dataSubtype,,, +representative,"An activity that stands as an equivalent of something or results in an equivalent; typical of, or the same as, others in a larger group of people or things.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C67045,dataSubtype,,, +raw counts,The number or amount of something.,,assay,FALSE,http://purl.obolibrary.org/obo/NCIT_C25463,dataType,,, +Volume,The amount of three dimensional space occupied by an object or the capacity of a space or container.,,assay,FALSE,http://purl.obolibrary.org/obo/NCIT_C25335,dataType,,, +Weight,The vertical force exerted by a mass as a result of gravity.,,assay,FALSE,http://purl.obolibrary.org/obo/NCIT_C25208,dataType,,, +Pharmacokinetic Study,"A study of the process by which a drug is absorbed, distributed, metabolized, and eliminated by the body.",,assay,FALSE,http://purl.obolibrary.org/obo/NCIT_C49663,dataType,,, +genomicVariants,"Genomic alterations, including single nucleotide polymorphisms, short indels and structural variants, in a genome sequence.",,assay,FALSE,https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Foperation_3227,dataType,,, +behavior process,"The action, reaction, or performance of an organism in response to external or internal stimuli.",,assay,FALSE,http://purl.obolibrary.org/obo/NBO_0000313,dataType,,, +metabolomics,"The systematic study of metabolites, the chemical processes they are involved, and the chemical fingerprints of specific cellular processes in a whole cell, tissue, organ or organism.",,assay,FALSE,http://edamontology.org/topic_3172,dataType,,, +image,Biological or biomedical data that has been rendered into an image.,,assay,FALSE,https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fdata_2968,dataType,,, +geneExpression,The analysis of levels and patterns of synthesis of gene products (proteins and functional RNA) including interpretation in functional terms of gene expression data.,,assay,FALSE,https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Ftopic_0203,dataType,,, +isoformExpression,Expression of protien isoforms formed from alternative splicings or other post-translational modifications of a single gene through RNA splicing mechanisms.,,assay,FALSE,https://en.wikipedia.org/wiki/Protein_isoform,dataType,,, +proteomics,"Protein and peptide identification, especially in the study of whole proteomes of organisms.",,assay,FALSE,https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Ftopic_0121,dataType,,, +kinomics,Kinomics is the study of protein kinases and protein kinase signaling.,,assay,FALSE,http://www.kinomecore.com/what-is-kinomics/,dataType,,, +drugScreen,Information on drug sensitivity and molecular markers of drug response,,assay,FALSE,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531057/,dataType,,, +drugCombinationScreen,Information on drug sensitivity of more than one compound,,,FALSE,https://www.ncbi.nlm.nih.gov/pubmed/29344898,dataType,,, +cellularPhysiology,,,assay,FALSE,,dataType,,, +chromatinActivity,Chromatin activity that allow access of condensed genomic DNA and potentially control gene expression.,,,FALSE,https://en.wikipedia.org/wiki/Chromatin_remodeling,dataType,,, +surveyData,A data set that contains the outcome of a survey.,,assay,FALSE,http://purl.obolibrary.org/obo/OMIABIS_0000060,dataType,,, +network,An interconnected system of things or people.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C61377,dataType,,, +clinical,Data obtained through patient examination or treatment.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C15783,dataType,,, +immunoassay,Laboratory test involving interaction of antigens with specific antibodies.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C16723,dataType,,, +electrophysiology,Data generated from an electrophysiology assay.,,,FALSE,http://purl.obolibrary.org/obo/ERO_0000564,dataType,,, +mask image,"Image used as the mask for an image processing operation, such as subtraction.",,,FALSE,http://dicom.nema.org/resources/ontology/DCM/121321,dataType,,, +Neurofibromatosis type 1,"(NF1) - A disease characterized by patches of skin pigmentation (cafe-au-lait spots), Lisch nodules of the iris, tumors in the peripheral nervous system and fibromatous skin tumors. Individuals with the disorder have increased susceptibility to the development of benign and malignant tumors.",,,FALSE,,diagnosis,,, +Neurofibromatosis type 2,"(NF2) - Genetic disorder characterized by bilateral vestibular schwannomas (formerly called acoustic neuromas), schwannomas of other cranial and peripheral nerves, meningiomas, and ependymomas. It is inherited in an autosomal dominant fashion with full penetrance.",,,FALSE,https://www.ebi.ac.uk/ols/ontologies/cco/terms?iri=http%3A%2F%2Fidentifiers.org%2Fomim%2F101000,diagnosis,,, +Schwannomatosis,A rare genetic disorder characterized by the presence of multiple schwannomas.,,,FALSE,https://www.ebi.ac.uk/ols/ontologies/ncit/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCIT_C6557,diagnosis,,, +Not Applicable,"An NF diagnosis (e.g. NF1, NF2, or Schwannomatosis) does not apply here.",,,FALSE,,diagnosis,,, +Sporadic Schwannoma,A,,,,,,,, +diagnosis,A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms.,"Neurofibromatosis type 1, Neurofibromatosis type 2, Schwannomatosis, Unknown, Not Applicable, Sporadic Schwannoma",,FALSE,,experimentalData,,, +10x_v2,,,,FALSE,https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json,dissociationMethod,,, +FACS,,,,FALSE,https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json,dissociationMethod,,, +Fluidigm C1,,,,FALSE,https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json,dissociationMethod,,, +drop-seq,,,,FALSE,https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json,dissociationMethod,,, +inDrop,,,,FALSE,https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json,dissociationMethod,,, +mouth pipette,,,,FALSE,https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json,dissociationMethod,,, +enzymatic,,,,FALSE,https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json,dissociationMethod,,, +mechanical,,,,FALSE,https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json,dissociationMethod,,, +singleMolecule,An experiment in which a single molecule was used in an assay,,,FALSE,,drugScreenType,,, +smallMoleculeLibraryScreen,"High throughput sample analysis of small molecules for purpose such as drug discovery, or biochemical, genetic or pharmacological tests.",,,FALSE,http://purl.obolibrary.org/obo/ERO_0001726,drugScreenType,,, +combinationLibraryScreen,High throughput sample analysis of collections of compounds that provide a variety of chemically diverse structures that can be used to identify structure types that have affinity with pharmacological targets.,,,FALSE,http://purl.obolibrary.org/obo/ERO_0001686,drugScreenType,,, +combinationScreen,,,,FALSE,,drugScreenType,,, +assay,The technology used to generate the data in this file,"elevated plus maze test, open field test, rotarod performance test, mRNAcounts, high content screen, Immunocytochemistry, immunofluorescence, autoradiography, electrochemiluminescence, Real Time PCR, in vivo tumor growth, scale, Blood Chemistry Measurement, in vivo bioluminescence, immunohistochemistry, NOMe-Seq, FIA-MSMS, UPLC-MSMS, HPLC-MSMS, liquid chromatography-electrochemical detection, rnaSeq, mirnaSeq, LC-MSMS, LC-MS, lncrnaSeq, Whole Exome Sequencing, Sanger sequencing, ChIPSeq, rnaArray, snpArray, methylationArray, mirnaArray, bisulfiteSeq, ATACSeq, HI-C, errBisulfiteSeq, ISOSeq, westernBlot, wholeGenomeSeq, polymeraseChainReaction, cellViabilityAssay, atomicForceMicroscopy, brightfieldMicroscopy, tractionForceMicroscopy, nextGenerationTargetedSequencing, jumpingLibrary, MIB/MS, scCGIseq, MudPIT, questionnaire, DNA optical mapping, oxBS-Seq, Ribo-Seq, Positron Emission Tomography, RPPA, ELISA, LTP, LFP, whole-cell patch clamp, sandwich ELISA, Laser Speckle Imaging, Genotyping, TMT quantitation, label free mass spectrometry, cell count, reporter gene assay, Single Cell RNA Sequencing, Conventional MRI, Functional MRI, Magnetic Resonance Spectroscopy",,TRUE,,experimentalData,,, +dataSubtype,"Further qualification of dataType, which may be used to indicate the state of processing of the data, aggregation of the data, or presence of metadata.","normalized, dataMatrix, raw, processed, metadata, representative",,TRUE,,experimentalData,,, +metadataType,"For files of dataSubtype: metadata, a description of the type of metadata in the file.","individual, biospecimen, assay, data dictionary, manifest, protocol",,FALSE,,experimentalData,,, +bodyPart,"Sample location referring to a named area of the body, inclusive of gross anatomical structures and organ parts. ","head, neck, scalp, leg, pelvis, mesentery, axilla, acetabulum, forearm, muscle, finger, thoracic spine, groin, back, iliac spine, spine, shoulder, scapula, lymph node, kidney, skin, mammary gland, nerves, brain, blood, breast, colon, lung, liver, prostate, pancreas, ovary, spleen, bone marrow, Bursa Of Fabricius, nose",,FALSE,,experimentalData,,, +organ,A unique macroscopic (gross) anatomic structure that performs specific functions. It is composed of various tissues. An organ is part of an anatomic system or a body region.,"lymph node, kidney, skin, mammary gland, nerves, brain, blood, breast, colon, lung, liver, prostate, pancreas, ovary, spleen, bone marrow, Bursa Of Fabricius, nose",,FALSE,,experimentalData,,, +dataType,"A type of experimental, clinical, or other data. This typically refers to a high-level data type, that is paired with a specific assay. For example, a file of dataType of ""genomicVariants"" might have an assay value of ""whole genome sequencing"". ","Volume, Weight, Pharmacokinetic Study, genomicVariants, behavior process, metabolomics, image, geneExpression, isoformExpression, proteomics, kinomics, drugScreen, drugCombinationScreen, cellularPhysiology, chromatinActivity, surveyData, network, clinical, immunoassay, electrophysiology, raw counts, mask image",,FALSE,,experimentalData,,, +individualIdSource,Database or repository to which individual ID maps,,,FALSE,,experimentalData,,, +tissue,A tissue is a mereologically maximal collection of cells that together perform physiological function.,"nerve tissue,optic nerve,serum,plasma,splenocyte,blood,primary tumor,embryonic tissue,meninges,bone marrow,Buccal Mucosa,Dorsal Root Ganglion,unspecified,whole brain,Buffy Coat,cerebral cortex,sciatic nerve,connective tissue,tumor-adjacent normal, PDX tissue, CDX tissue, metastatic/recurrent tumor, recurrent tumor, metastatic tumor",,FALSE,,experimentalData,,, +platform,"A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","HiSeq3000, HiSeq2500, HiSeq4000, NextSeq500, HiSeq2000, MiSeq, Zeiss LSM 980, Affy5.0, Affy6.0, PacBioRSII, GAIIx, Illumina_HumanOmni1-Quadv1.0, Illumina_1M, Illumina_h650, Illumina_Omni2pt5M, Illumina_Omni5M, Illumina MouseWG-6 v2.0 expression beadchip, Perlegen300Karray, Agilent44Karray, IlluminaWholeGenomeDASL, IlluminaHumanHap300, NanostringnCounter, LTQOrbitrapXL, IlluminaHumanMethylation450, Illumina Infinium MethylationEPIC BeadChip, AffymetrixU133AB, Affymetrix Human Gene 1.0 ST Array, AffymetrixU133Plus2, HiSeqX, Bionano Irys, Infinium HumanOmniExpressExome, NextSeq 550, NextSeq 1000, NextSeq 2000, PacBio Sequel IIe System, PacBio Sequel II System, NanostringGeoMx, LI-COR Odyssey CLx, Spectramax M Series, Olympus DP80, Orbitrap Fusion Lumos Tribrid, Illumina_NovaSeq_6000",,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group&anchor=platform,experimentalData,,, +isCellLine,Boolean flag indicating whether or not sample source is a cell line. (Note: TRUE = Yes; FALSE = No),"TRUE, FALSE",,FALSE,,experimentalData,,, +isPrimaryCell,Boolean flag indicating whether or not cellType is primary (Note: TRUE = Yes; FALSE = No),"TRUE, FALSE",,FALSE,,experimentalData,,, +cellType,A cell type is a distinct morphological or functional form of cell.,"Schwann cell precusor, B-lymphocytes, Embryonic stem cells, iPSC, iPSC-derived telencephalic organoids, GABAergic neurons, monocytes, microglia, macrophages, astrocytes, SH-SY5Y, GLUtamatergic neurons, NeuN+, NeuN-, epithelial, epithelial-like, fibroblast, round, lymphoblast, polygonal, CD8+ T-Cells, arachnoid, meningioma, schwannoma, oligodendrocyte, schwann, iPSC-derived neuron, iPSC-derived glia, iPSC-derived astrocytes, monocyte-derived microglia, iPSC-derived neuronal progenitor cell, CD138+, CNON, teratoma",,FALSE,,experimentalData,,, +isMultiIndividual,Boolean flag indicating whether or not a file has data for multiple individuals (Note: TRUE = Yes; FALSE = No),"TRUE, FALSE",,TRUE,,experimentalData,,, +isMultiSpecimen,Boolean flag indicating whether or not a file has data for multiple specimens (Note: TRUE = Yes; FALSE = No),"TRUE, FALSE",,TRUE,,experimentalData,,, +sex,"Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","Male, Female, Unknown",,FALSE,http://purl.obolibrary.org/obo/NCIT_C28421,experimentalData,,, +Male,"A person who belongs to the sex that normally produces sperm. The term is used to indicate biological sex distinctions, cultural gender role distinctions, or both.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C20197,sex,,, +Female,"A person who belongs to the sex that normally produces ova. The term is used to indicate biological sex distinctions, or cultural gender role distinctions, or both.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C16576,sex,,, +Unknown,"Not known, observed, recorded; or reported as unknown by the data contributor.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C17998,sex,,, +species,The name of a species (typically a taxonomic group) of organism.,"Homo sapiens,Mus musculus,Mus musculus (humanized),Rattus norvegicus,Drosophila melanogaster,Rhesus macaque,Pan troglodytes,Gallus gallus,Sus scrofa,Oryctolagus cuniculus,Danio rerio",,FALSE,,experimentalData,,, +failedQC,Boolean flag indicating whether the sample or data failed QC checks (Note: TRUE = Yes; FALSE = No),"TRUE, FALSE",,TRUE,,experimentalData,,, +individualID,A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID. ,,,FALSE,,experimentalData,,, +specimenID,A unique identifier (non-PII) that represents the specimen (sample) from which the data came. e.g. an ID that indicates a specific tumor specimen.,,,FALSE,,experimentalData,,, +libraryID,,,,TRUE,,experimentalData,,, +assayTarget,The HUGO gene symbol that represents the target analyte assayed.,,,FALSE,Sage Bionetworks,experimentalData,,, +proteinExtractSource,Source of the extracted protein used in the experiment,"cell lysate, nuclei, mitochondria, cytoplasm",,TRUE,http://purl.obolibrary.org/obo/OBI_0000894,experimentalData,,, +reporterGene,"A biological material (clone, oligo, etc.) on an array which will report on some biosequence or biosequences.",,,FALSE,,experimentalData,,, +reporterSubstance,A gene which produces an easily assayed phenotype. Often used for expression studies of heterologous promoters.,,,FALSE,,experimentalData,,, +bash script,Bash Shell Script,,,FALSE,https://en.wikipedia.org/wiki/Shell_script,fileFormat,,, +bedgraph,Holds a tab-delimited chromosome /start /end / datavalue dataset. The bedGraph format allows display of continuous-valued data in track format. This display type is useful for probability scores and transcriptome data,,,FALSE,http://edamontology.org/format_3583,fileFormat,,, +ai,Adobe Illustrator format,,,FALSE,http://www.ebi.ac.uk/swo/data/SWO_3000023,fileFormat,,, +idx,,,,FALSE,,fileFormat,,, +idat,Proprietary file format for (raw) BeadArray data used by genomewide profiling platforms from Illumina Inc. This format is output directly from the scanner and stores summary intensities for each probe-type on an array.,,,FALSE,http://edamontology.org/format_3578,fileFormat,,, +bam,"BAM format, the binary, BGZF-formatted compressed version of SAM format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s)",,,FALSE,http://edamontology.org/format_2572,fileFormat,,, +bai,BAM indexing format,,,FALSE,http://edamontology.org/format_3327,fileFormat,,, +excel,Microsoft Excel spreadsheet format,,,FALSE,,fileFormat,,, +powerpoint,Microsoft Powerpoint slide format,,,FALSE,,fileFormat,,, +tif,"Tagged Image File Format, abbreviated TIFF or TIF, is a computer file format for storing raster graphics images",,,FALSE,https://en.wikipedia.org/wiki/TIFF,fileFormat,,, +png,PNG is a file format for image compression,,,FALSE,http://edamontology.org/format_3603,fileFormat,,, +doc,Microsoft Word document format,,,FALSE,,fileFormat,,, +pdf,Portable Document Format,,,FALSE,http://edamontology.org/format_3508,fileFormat,,, +hdf,"Hierarchical Data Format (HDF) is a set of file formats (HDF4, HDF5) designed to store and organize large amounts of data",,,FALSE,https://en.wikipedia.org/wiki/Hierarchical_Data_Format,fileFormat,,, +fasta,"FASTA format is a text-based format for representing either nucleotide sequences or peptide sequences, in which nucleotides or amino acids are represented using single-letter codes",,,FALSE,https://en.wikipedia.org/wiki/FASTA_format,fileFormat,,, +fastq,FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. Both the sequence letter and quality score are each encoded with a single ASCII character for brevity,,,FALSE,https://en.wikipedia.org/wiki/FASTQ_format,fileFormat,,, +sam,Sequence Alignment/Map (SAM) format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s),,,FALSE,http://edamontology.org/format_2573,fileFormat,,, +vcf,"Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation)",,,FALSE,http://edamontology.org/format_3016,fileFormat,,, +bcf,"BCF, the binary version of Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation)",,,FALSE,http://edamontology.org/format_3016,fileFormat,,, +maf,"Multiple Alignment Format (MAF) supporting alignments of whole genomes with rearrangements, directions, multiple pieces to the alignment, and so forth",,,FALSE,http://edamontology.org/format_3008,fileFormat,,, +bed,"Browser Extensible Data (BED) format of sequence annotation track, typically to be displayed in a genome browser",,,FALSE,http://edamontology.org/format_3003,fileFormat,,, +chp,CHP file contains probe set analysis results generated from Affymetrix software,,,FALSE,,fileFormat,,, +cel,Format of Affymetrix data file of information about (raw) expression levels of the individual probes,,,FALSE,http://edamontology.org/format_1638,fileFormat,,, +sif,SIF (simple interaction file) Format - a network/pathway format used for instance in cytoscape,,,FALSE,http://edamontology.org/format_3619,fileFormat,,, +tsv,Tabular data represented as tab-separated values in a text file,,,FALSE,http://edamontology.org/format_3475,fileFormat,,, +csv,Tabular data represented as comma-separated values in a text file,,,FALSE,http://edamontology.org/format_3752,fileFormat,,, +txt,Textual format,,,FALSE,http://edamontology.org/format_2330,fileFormat,,, +plink,Any Plink file format (MAP/PED/BED/BIM/FAM),,,FALSE,https://www.cog-genomics.org/plink2/formats,fileFormat,,, +bigwig,bigWig format for large sequence annotation tracks that consist of a value for each sequence position,,,FALSE,http://edamontology.org/format_3006,fileFormat,,, +wiggle,Wiggle format (WIG) of a sequence annotation track that consists of a value for each sequence position,,,FALSE,http://edamontology.org/format_3005,fileFormat,,, +gct,"Tab-delimited text files of GenePattern that contain a column for each sample, a row for each gene, and an expression value for each gene in each sample",,,FALSE,http://edamontology.org/format_3709,fileFormat,,, +bgzip,Blocked GNU Zip format,,,FALSE,http://edamontology.org/format_3615,fileFormat,,, +zip,zip is a format standard of a digital entity that is conformant with the PKWARE .ZIP file format specification,,,FALSE,http://purl.obolibrary.org/obo/OBI_0000325,fileFormat,,, +seg,SEG file (segmented data; .seg or .cbs) is a tab-delimited text file that lists loci and associated numeric values,,,FALSE,https://software.broadinstitute.org/software/igv/SEG,fileFormat,,, +html,HTML format,,,FALSE,http://edamontology.org/format_2331,fileFormat,,, +mov,A video file format with the .mov extension,,,FALSE,Sage Bioenetworks,fileFormat,,, +hyperlink,"A reference (link) from some point in one hypertext document to another document, another place in the same document, or a website.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C47919,fileFormat,,, +svs,"A single-file pyramidal tiled TIFF, with non-standard metadata and compression.",,,FALSE,https://openslide.org/formats/aperio/,fileFormat,,, +md,Markdown (MD) is a lightweight markup language with plain text formatting syntax,,,FALSE,https://en.wikipedia.org/wiki/Markdown,fileFormat,,, +flagstat,Output of samtools flagstat tool,,,FALSE,,fileFormat,,, +gtf,Gene transfer format (GTF) is a file format used to hold information about gene structure,,,FALSE,https://en.wikipedia.org/wiki/Gene_transfer_format,fileFormat,,, +raw,Proprietary file format for mass spectrometry data from Thermo Scientific,,,FALSE,http://edamontology.org/format_3712,fileFormat,,, +msf,Proprietary mass-spectrometry format of Thermo Scientific's ProteomeDiscoverer software,,,FALSE,http://edamontology.org/format_3702,fileFormat,,, +rmd,markdown document specific to r analyses,,,FALSE,http://rmarkdown.rstudio.com/developer_document_templates.html,fileFormat,,, +bed narrowPeak,"This format is used to provide called peaks of signal enrichment based on pooled, normalized (interpreted) data. It is a BED6+4 format.",,,FALSE,http://genome.ucsc.edu/FAQ/FAQformat.html#format12,fileFormat,,, +bed broadPeak,"This format is used to provide called regions of signal enrichment based on pooled, normalized (interpreted) data. It is a BED 6+3 format.",,,FALSE,http://genome.ucsc.edu/FAQ/FAQformat.html#format13,fileFormat,,, +bed gappedPeak,"This format is used to provide called regions of signal enrichment based on pooled, normalized (interpreted) data where the regions may be spliced or incorporate gaps in the genomic sequence. It is a BED12+3 format.",,,FALSE,http://genome.ucsc.edu/FAQ/FAQformat.html#format14,fileFormat,,, +avi,AVI files can contain both audio and video data in a file container that allows synchronous audio-with-video playback.,,,FALSE,https://en.wikipedia.org/wiki/Audio_Video_Interleave,fileFormat,,, +pzfx,"A PZFX file is a Prism project created by GraphPad Prism, a scientific application used to analyze and graph data. It contains project data including graphs and layouts, notes, and tables.",,,FALSE,https://fileinfo.com/extension/pzfx,fileFormat,,, +fig,"Line drawing saved in the Xfig format; stored as a vector image that may include lines, shapes, arcs, splines, arrows, and text objects; may also include images, colors, and patterns.",,,FALSE,https://fileinfo.com/extension/fig,fileFormat,,, +xml,eXtensible Markup Language (XML) format.,,,FALSE,http://edamontology.org/format_2332,fileFormat,,, +tar,tape archive,,,FALSE,https://en.wikipedia.org/wiki/Tar_(computing),fileFormat,,, +R script,R Script,,,FALSE,Sage Bionetworks,fileFormat,,, +abf,The Axon Binary File format (ABF) was created for the storage of binary experimental data.,,,FALSE,https://mdc.custhelp.com/euf/assets/content/ABFHelp.pdf,fileFormat,,, +bpm,A beaded pool manifest. Describe the SNP or probe content on a BeadChip or in an assay pool.,,,FALSE,https://support.illumina.com/datafiles.html,fileFormat,,, +dat,Format of Affymetrix data file of raw image data.,,,FALSE,http://edamontology.org/format_1637,fileFormat,,, +jpg,Joint Picture Group file format for lossy graphics file.,,,FALSE,http://edamontology.org/format_3579,fileFormat,,, +locs,Illumina iScan bead location file.,,,FALSE,https://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/iscan/iscan-system-guide-11313539-01.pdf,fileFormat,,, +Sentrix descriptor file,A BeadScan specific file needed to perform scan setting checks for different array formats and assay type.,,,FALSE,https://support.illumina.com/content/dam/illumina-support/documents/myillumina/dd0aff11-2664-481b-a8ce-26831a907cae/beadscan_3.0_software_addendum.pdf,fileFormat,,, +Python script,"Python is an interpreted, object-oriented, high-level programming language with dynamic semantics.",,,FALSE,https://www.python.org/doc/essays/blurb/,fileFormat,,, +sav,"The SPSS Statistics File Format is a proprietary binary format, developed and maintained as the native format for the SPSS statistical software application.",,,FALSE,https://www.loc.gov/preservation/digital/formats/fdd/fdd000469.shtml,fileFormat,,, +gzip,GZipped format,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C80220,fileFormat,,, +sdf,SDF is one of a family of chemical-data file formats developed by MDL Information Systems; it is intended especially for structural information.,,,FALSE,http://edamontology.org/format_3814,fileFormat,,, +RData,"The RData format (usually with extension .rdata or .rda) is a format designed for use with R, a system for statistical computation and related graphics, for storing a complete R workspace or selected 'objects' from a workspace in a form that can be loaded back by R.",,,FALSE,https://www.loc.gov/preservation/digital/formats/fdd/fdd000470.shtml,fileFormat,,, +hic,Hi-C contact matrix file,,,FALSE,https://github.com/theaidenlab/juicer/wiki/Data,fileFormat,,, +ab1,TAB1 binary format of raw DNA sequence reads (output of Applied Biosystems' sequencing analysis software). Contains an electropherogram and the DNA base sequence.,,,FALSE,http://edamontology.org/format_3000,fileFormat,,, +7z,"A compressed archive file format that supports several different data compression, encryption and pre-processing filters.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C80224,fileFormat,,, +gff3,Generic Feature Format version 3 (GFF3) of sequence features.,,,FALSE,http://edamontology.org/format_1975,fileFormat,,, +json,"JavaScript Object Notation format; a lightweight, text-based format to represent tree-structured data using key-value pairs.",,,FALSE,http://edamontology.org/format_3464,fileFormat,,, +sqlite,Data format used by the SQLite database.,,,FALSE,http://edamontology.org/format_3621,fileFormat,,, +svg,Scalable Vector Graphics (SVG) is an XML-based vector image format for two-dimensional graphics with support for interactivity and animation.,,,FALSE,http://edamontology.org/format_3604,fileFormat,,, +sra,SRA archive format (SRA) is the archive format used for input to the NCBI Sequence Read Archive.,,,FALSE,http://edamontology.org/format_3698,fileFormat,,, +recal,.recal file from GATK VQSR,,,FALSE,https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_variantrecalibration_VariantRecalibrator.php#--recal_file,fileFormat,,, +tranches,.tranches file from GATK VQSR,,,FALSE,https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_variantrecalibration_VariantRecalibrator.php#--tranches_file,fileFormat,,, +mtx,Matrix Market Exchange Format,,,FALSE,https://math.nist.gov/MatrixMarket/formats.html#MMformat,fileFormat,,, +tagAlign,Tag Alignment provides genomic mapping of short sequence tags.,,,FALSE,https://genome.ucsc.edu/FAQ/FAQformat.html#format15,fileFormat,,, +dup,output of the Picard MarkDuplicates tool.,,,FALSE,https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.4.0/picard_sam_markduplicates_MarkDuplicates.php,fileFormat,,, +DICOM,"A comprehensive set of standards for communications between medical imaging devices, including handling, storing and transmitting information in medical imaging. It includes a file format definition and a network communication protocol.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C49059,fileFormat,,, +czi,"microscopy imaging file format that saves multidimensional images such as time lapse, Z-stacks, multiposition experiments and virtual slides, combined with relevant meta information",,,FALSE,https://www.zeiss.com/microscopy/int/products/microscope-software/zen/czi.html,fileFormat,,, +mzML,"mzML format for raw spectrometer output data, standardised by HUPO PSI MSS.",,,FALSE,http://edamontology.org/format_3244,fileFormat,,, +SPAR,Phillips MRS Header File,,,FALSE,https://github.com/chenkonturek/MRS_MRI_libs,fileFormat,,, +SDAT,Phillips MRS Data File,,,FALSE,https://github.com/chenkonturek/MRS_MRI_libs,fileFormat,,, +nii,"NIfTI-1 can store image data from any modality such as PET, MRI, CT, EEG that produces regularly sampled 1-5D rasters.",,,FALSE,https://nifti.nimh.nih.gov/nifti-1/documentation/faq,fileFormat,,, +PAR," +This is yet another MRI image format generated by Philips scanners. It is an ASCII header (PAR) plus a binary blob (REC).",,,FALSE,https://nipy.org/nibabel/reference/nibabel.parrec.html,fileFormat,,, +REC,This is yet another MRI image format generated by Philips scanners. It is an ASCII header (PAR) plus a binary blob (REC).,,,FALSE,https://nipy.org/nibabel/reference/nibabel.parrec.html,fileFormat,,, +hdr,"MRI Header file, as in the NIFTI-1 Analyze 7.5 format",,,FALSE,https://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1.h,fileFormat,,, +img,"MRI Data file, as in the NIFTI-1 Analyze 7.5 format",,,FALSE,https://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1.h,fileFormat,,, +sf,"Salmon’s main output is its quantification file. This file is a plain-text, tab-separated file with a single header line (which names all of the columns).",,,FALSE,https://salmon.readthedocs.io/en/latest/file_formats.html,fileFormat,,, +RNAi,High throughput sample analysis of RNAi molecules for potential application in gene knockdown or gene silencing of target genes,,,FALSE,http://purl.obolibrary.org/obo/ERO_0001688,genePerturbationTechnology,,, +CRISPR,,,,FALSE,,genePerturbationTechnology,,, +CRE Recombinase,CRE Recombinase catalyses site-specific recombination between two 34 base pair loxp sites and maintains the phage genome as a monomeric unit-copy plasmid in the lysogenic state.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C17285,genePerturbationTechnology,,, +overexpression,Gene overexpression refers to genetic techniques in which an organism or cell line is engineered to express increased levels of a gene.,,,FALSE,http://www.bioassayontology.org/bao#BAO_0002442,genePerturbationType,,, +knockdown,"Gene knockdown refers to techniques by which the expression of one or more of an organism's genes is reduced, either through genetic modification (a change in the DNA of one of the organism's chromosomes) or by treatment with a reagent such as a short DNA or RNA oligonucleotide with a sequence complementary to either an mRNA transcript or a gene.",,,FALSE,http://www.bioassayontology.org/bao#BAO_0002433,genePerturbationType,,, +knockout,A gene knockout is a genetic technique in which an organism is engineered to carry genes that have been made inoperative (have been 'knocked out' of the organism).,,,FALSE,http://www.bioassayontology.org/bao#BAO_0002441,genePerturbationType,,, +immunoAssayType,Type of immuno assay,"ChIPseq, ATAC-seq",,TRUE,,immunoAssay,,, +ChIPSeq,AMP-AD ChIPseq immunology assay,,,FALSE,,immunoAssay,,, +JAX,The Jackson Laboratory,,,FALSE,https://www.jax.org,individualIdSource,,, +rRNAdepletion,Total RNA library with ribosomal RNA depleted.,,,FALSE,Sage Bionetworks,libraryPrep,,, +polyAselection,RNA selection by polyA tail capture,,,FALSE,Sage Bionetworks,libraryPrep,,, +lncRNAenrichment,RNA library enriched for lncRNA,,,FALSE,Sage Bionetworks,libraryPrep,,, +miRNAenrichment,RNA library with size selection for microRNAs,,,FALSE,Sage Bionetworks,libraryPrep,,, +10x,10x Genomics library preparation,,,FALSE,https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json,libraryPreparationMethod,,, +CEL-seq,CEL-Seq library preparation,,,FALSE,https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json,libraryPreparationMethod,,, +Drop-Seq,Drop-Seq library preparation,,,FALSE,https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json,libraryPreparationMethod,,, +Smart-seq2,Smart-seq 2 library preparation,,,FALSE,https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json,libraryPreparationMethod,,, +TruSeq,TruSeq library preparation,,,FALSE,https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json,libraryPreparationMethod,,, +Smart-seq4,Smart-seq4 library preparation,,,FALSE,https://www.takarabio.com/products/next-generation-sequencing/single-cell-rna-and-dna-seq/smart-seq-v4-for-mrna-seq,libraryPreparationMethod,,, +Omni-ATAC,Omni-ATAC-seq library preparation,,,FALSE,https://protocolexchange.researchsquare.com/article/nprot-6107/v1,libraryPreparationMethod,,, +NEBNext mRNA Library Prep Reagent Set for Illumina,NEBNext mRNA Library Prep Reagent Set for Illumina,,,FALSE,https://www.neb.com/products/e6100-nebnext-mrna-library-prep-reagent-set-for-illumina,libraryPreparationMethod,,, +IDT xGen Exome Research Panel,,,,FALSE,https://www.idtdna.com/pages/products/next-generation-sequencing/targeted-sequencing/hybridization-capture/predesigned-panels/xgen-exome-research-panel-v2,libraryPreparationMethod,,, +individual,Metadata describing properties of individuals (human or animal) represented in the study.,,,FALSE,Sage Bionetworks,metadataType,,, +biospecimen,Metadata describing properties of specimens collected and/or analyzed in the study.,,,FALSE,Sage Bionetworks,metadataType,,, +assay,Metadata describing properties of an assay conducted in the study.,,,FALSE,Sage Bionetworks,metadataType,,, +data dictionary,Metadata describing terms or variables that appear in another file.,,,FALSE,Sage Bionetworks,metadataType,,, +manifest,Metadata describing a list of files and the annotations terms associated with them.,,,FALSE,Sage Bionetworks,metadataType,,, +protocol,"A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.",,,FALSE,http://purl.obolibrary.org/obo/OBI_0000272,metadataType,,, +C57BL/6J,C57BL/6 is the most widely used inbred strain. It is commonly used as a general purpose strain and background strain for the generation of congenics carrying both spontaneous and induced mutations.,,,FALSE,https://www.jax.org/strain/000664,modelSystemName,,, +NOD scid gamma,"These mice are most often referred to using their branded name ""NSG™"" and are extremely immunodeficient.",,,FALSE,https://www.jax.org/strain/005557,modelSystemName,,, +B6;129S2-Trp53tm1Tyj Nf1tm1Tyj/J,,,,FALSE,https://www.jax.org/strain/008191,modelSystemName,,, +B6;129-Trp53tm1Tyj Nf1tm1Tyj Suz12Gt(Betageo)1Khe/KcichJ,,,,FALSE,https://www.jax.org/strain/027678,modelSystemName,,, +B6.129S2-Nf1tm1Tyj/J,,,,FALSE,https://www.jax.org/strain/008192,modelSystemName,,, +B6.129S1-Nf1tm1Cbr/J,,,,FALSE,https://www.jax.org/strain/007923,modelSystemName,,, +B6.129(Cg)-Nf1tm1Par/J,,,,FALSE,https://www.jax.org/strain/017640,modelSystemName,,, +hiPSC-SCP,Schwann cell precursor iPSCs,,,FALSE,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7773354,modelSystemName,,, +hiPSC,human iPSCs,,,FALSE,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7773355,modelSystemName,,, +JHU 2-103-CL,An MPNST cell line derived from JHU NF1 Biobank tumor specimen JHU 2-103. ,,,FALSE,Sage Bionetworks,modelSystemName,,, +JHU 2-002-CL,An MPNST cell line derived from JHU NF1 Biobank tumor specimen JHU 2-002. ,,,FALSE,Sage Bionetworks,modelSystemName,,, +JHU 2-079-CL,An MPNST cell line derived from JHU NF1 Biobank tumor specimen JHU 2-079. ,,,FALSE,Sage Bionetworks,modelSystemName,,, +JHU 2-103-PDX,A PDX model derived from JHU NF1 Biobank tumor specimen JHU 2-103. ,,,FALSE,Sage Bionetworks,modelSystemName,,, +JHU 2-002-PDX,A PDX model derived from JHU NF1 Biobank tumor specimen JHU 2-002. ,,,FALSE,Sage Bionetworks,modelSystemName,,, +JHU 2-079-PDX,A PDX model derived from JHU NF1 Biobank tumor specimen JHU 2-079. ,,,FALSE,Sage Bionetworks,modelSystemName,,, +human foreskin fibroblasts,"generic human foreskin fibroblasts, often used as a control cell in toxicology experiments",,,FALSE,Sage Bionetworks,modelSystemName,,, +hTERT NF1 ipNF05.5,plexiform neurofibroma cell line,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_UI71,modelSystemName,,, +hTERT NF1 ipNF05.5 (Mixed clones),plexiform neurofibroma cell line,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_UI72,modelSystemName,,, +hTERT NF1 ipn06.2 A,plexiform neurofibroma cell line,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_UI74,modelSystemName,,, +hTERT NF1 ipNF95.11b C/T,plexiform neurofibroma cell line,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_UI68,modelSystemName,,, +hTERT NF1 ipNF95.6,plexiform neurofibroma cell line,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_UI70,modelSystemName,,, +hTERT SC ipn02.8,plexiform neurofibroma cell line,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_UI65,modelSystemName,,, +hTERT NF1 ipnNF95.11c,plexiform neurofibroma cell line,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_UI69,modelSystemName,,, +hTERT NF1 ipNF95.11b C,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_UI67,modelSystemName,,, +hTERT NF1 ipnNF09.4,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_UI73,modelSystemName,,, +hTERT NF1 ipNF04.4,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_UI78,modelSystemName,,, +hTERT NF1 sipnNF95.12B,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_UI75,modelSystemName,,, +hTERT NF1 ipNF00.6,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_UI76,modelSystemName,,, +hTERT NF1 ipNF03.3,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_UI77,modelSystemName,,, +hTERT NF1 ipn02.3 2λ,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_UI64,modelSystemName,,, +hTERT SC ipn02.8,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_UI65,modelSystemName,,, +SZ-NF1,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_YL57,modelSystemName,,, +SZ-NF2,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_YL58,modelSystemName,,, +SZ-NF4,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_YL59,modelSystemName,,, +NF1,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_JG80,modelSystemName,,, +Lis42_NF1_1N,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_Y368,modelSystemName,,, +Lis47_NF1_2N,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_Y373,modelSystemName,,, +ST88-14,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_8916,modelSystemName,,, +sNF96.2,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_K281,modelSystemName,,, +sNF02.2,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_K280,modelSystemName,,, +sNF94.3,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_K164,modelSystemName,,, +GM11602,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_AA02,modelSystemName,,, +GM11601,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_AA01,modelSystemName,,, +KCL024,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_A257,modelSystemName,,, +KCL025,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_A258,modelSystemName,,, +5PNF_TDiPSsv_PM_6,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_UN14,modelSystemName,,, +5PNF_TDiPSsv_MM_4,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_UN13,modelSystemName,,, +7PNF_SiPSrv_PM_12,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_UN16,modelSystemName,,, +6PNF_SiPSrv_PM_2,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_UN15,modelSystemName,,, +3PNF_SiPSsv_MM_11,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_UN12,modelSystemName,,, +3PNF_FiPSsv_PM_2,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_UN11,modelSystemName,,, +NCC-MPNST5-C1,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_YU17,modelSystemName,,, +NCC-MPNST3-C1,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_YU14,modelSystemName,,, +NCC-MPNST4-C1,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_YU16,modelSystemName,,, +NCC-MPNST3-X2-C1,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_YU15,modelSystemName,,, +NCC-MPNST2-C1,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_YU13,modelSystemName,,, +STS-26T,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_8917,modelSystemName,,, +YST-1,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_5192,modelSystemName,,, +90-8,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_1B47,modelSystemName,,, +S520,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_AX35,modelSystemName,,, +S462,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_1Y70,modelSystemName,,, +S462.TY,,,,FALSE,"https://web.expasy.org/cellosaurus/VCL_JK02 +",modelSystemName,,, +T265,,,,FALSE,https://web.expasy.org/cellosaurus/CVCL_S805,modelSystemName,,, +modelSystemName,"A group of presumed common ancestry with clear-cut physiological but usually not morphological distinctions such as an animal model or cell line. EXAMPLE(S): HEK293T (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","C57BL/6J,NOD scid gamma,B6;129S2-Trp53tm1Tyj Nf1tm1Tyj/J,B6;129-Trp53tm1Tyj Nf1tm1Tyj Suz12Gt(Betageo)1Khe/KcichJ,B6.129S2-Nf1tm1Tyj/J,B6.129S1-Nf1tm1Cbr/J,B6.129(Cg)-Nf1tm1Par/J,hiPSC-SCP,hiPSC,JHU 2-103-CL,JHU 2-002-CL,JHU 2-079-CL,JHU 2-103-PDX,JHU 2-002-PDX,JHU 2-079-PDX,human foreskin fibroblasts,hTERT NF1 ipNF05.5,hTERT NF1 ipNF05.5 (Mixed clones),hTERT NF1 ipn06.2 A,hTERT NF1 ipNF95.11b C/T,hTERT NF1 ipNF95.6,hTERT SC ipn02.8,hTERT NF1 ipnNF95.11c,hTERT NF1 ipNF95.11b C,hTERT NF1 ipnNF09.4,hTERT NF1 ipNF04.4,hTERT NF1 sipnNF95.12B,hTERT NF1 ipNF00.6,hTERT NF1 ipNF03.3,hTERT NF1 ipn02.3 2λ,hTERT SC ipn02.8,SZ-NF1,SZ-NF2,SZ-NF4,NF1,Lis42_NF1_1N,Lis47_NF1_2N,ST88-14,sNF96.2,sNF02.2,sNF94.3,GM11602,GM11601,KCL024,KCL025,5PNF_TDiPSsv_PM_6,5PNF_TDiPSsv_MM_4,7PNF_SiPSrv_PM_12,6PNF_SiPSrv_PM_2,3PNF_SiPSsv_MM_11,3PNF_FiPSsv_PM_2,NCC-MPNST5-C1,NCC-MPNST3-C1,NCC-MPNST4-C1,NCC-MPNST3-X2-C1,NCC-MPNST2-C1,STS-26T,YST-1,90-8,S520,S462,S462.TY",,FALSE,http://purl.obolibrary.org/obo/NCIT_C94171,neuro,,, +Prss56Cre;R26mT,"Prss56Cre;R26mT is a transgenic non-human animal model for Neurofibromatosis type 1, wherein the Nf1 gene is specifically inactivated in BC cells and derivatives thereof.",,,FALSE,https://patents.google.com/patent/EP3420811A1/en,modelSystemName,,, +Nf1-OPG,,,,FALSE,,modelSystemName,,, +Nf1-OPG-Arg816,,,,FALSE,,modelSystemName,,, +nf2Genotype,"Genotype of NF2 gene in the biospecimen from which the data were derived, if known","-/-, +/-, +/+, +/?, -/?, Unknown",,FALSE,,neurofibromatosis,,, +nf1Genotype,"Genotype of NF1 gene in the biospecimen from which the data were derived, if known","-/-, +/-, +/+, +/?, -/?, Unknown",,FALSE,,neurofibromatosis,,, +genomicsAssay,"An assay of genomic type (rnaseq, exomeseq, etc). ",,"Filename,progressReportNumber,fileFormat,resourceType,dataType,dataSubtype,assay,individualID,sex,species,modelSystemName,modelSystemStrainNomenclature,genePerturbationType,genePerturbationTechnology,genePerturbed,diagnosis,specimenID,organ,tissue,nf1Genotype,nf2Genotype,isCellLine,isPrimaryCell,cellType,tumorType,specimenPreparationMethod,experimentalCondition,experimentalTimepoint,timePointUnit,platform,runType,readPair,isStranded,readPairOrientation,readStrandOrigin,libraryPrep,libraryPreparationMethod,nucleicAcidSource,dissociationMethod,readLength,readDepth,comments",TRUE,,template,,ngs, +imagingAssay,"An assay of imaging type (ihc, etc). ",,"Filename,progressReportNumber,fileFormat,resourceType,dataType,dataSubtype,assay,individualID,sex,species,modelSystemName,genePerturbationType,genePerturbationTechnology,genePerturbed,diagnosis,specimenID,organ,tissue,nf1Genotype,nf2Genotype,isCellLine,isPrimaryCell,cellType,tumorType,assayTarget,experimentalCondition,experimentalTimepoint,timePointUnit,platform,comments",TRUE,,template,,, +MRIAssay,,,"Filename,progressReportNumber,fileFormat,resourceType,dataType,dataSubtype,assay,individualID,sex,species,modelSystemName,diagnosis,specimenID,organ,tissue,nf1Genotype,nf2Genotype,experimentalCondition,experimentalTimepoint,timePointUnit,platform,MRISequence,comments",TRUE,,template,,, +Filename,The name of the file. ,,,TRUE,,NF,,, +epigeneticsAssay,An epigenetics assay. ,,"Filename,progressReportNumber,fileFormat,resourceType,dataType,dataSubtype,assay,individualID,sex,species,modelSystemName,genePerturbationType,genePerturbationTechnology,genePerturbed,diagnosis,specimenID,organ,tissue,nf1Genotype,nf2Genotype,isCellLine,isPrimaryCell,cellType,tumorType,assayTarget,experimentalCondition,experimentalTimepoint,timePointUnit,platform,readDepth,nucleicAcidSource,comments",TRUE,,template,,, +pharmacokineticsAssay,A pharmacokinetics assay. ,,"Filename,progressReportNumber,fileFormat,resourceType,dataType,dataSubtype,assay,individualID,sex,species,modelSystemName,genePerturbationType,genePerturbationTechnology,genePerturbed,diagnosis,specimenID,organ,tissue,nf1Genotype,nf2Genotype,isCellLine,isPrimaryCell,cellType,tumorType,assayTarget,experimentalCondition,experimentalTimepoint,timePointUnit,comments",TRUE,,template,,, +proteomicsAssay,A proteomics assay.,,"Filename,progressReportNumber,fileFormat,resourceType,dataType,dataSubtype,assay,individualID,sex,species,modelSystemName,genePerturbationType,genePerturbationTechnology,genePerturbed,diagnosis,specimenID,proteinExtractSource,organ,tissue,nf1Genotype,nf2Genotype,isCellLine,isPrimaryCell,cellType,tumorType,experimentalCondition,experimentalTimepoint,timePointUnit,platform,comments",TRUE,,template,,, +plateBasedReporterAssay,A plate based reporter assay. ,,"Filename,progressReportNumber,fileFormat,resourceType,dataType,dataSubtype,individualID,specimenID,sex,species,modelSystemName,genePerturbationType,genePerturbationTechnology,genePerturbed,diagnosis,organ,tissue,nf1Genotype,nf2Genotype,isCellLine,isPrimaryCell,cellType,tumorType,assay,platform,reporterGene,reporterSubstance,experimentalCondition,experimentalTimepoint,timePointUnit,comments",TRUE,,template,,, +patientTimepoints,Patient level metadata. Not for annotation.,,"individualID,sex,species,diagnosis,nf1Genotype,nf2Genotype,experimentalCondition,experimentalTimepoint,timePointUnit,comments",TRUE,,template,,, +-/-,Homozygous deletion or mutation of NF1.,,,FALSE,Sage Bionetworks,nf1Genotype,,, ++/-,Heterozygous deletion or mutation,,,FALSE,Sage Bionetworks,nf1Genotype,,, ++/+,Homozygous wildtype,,,FALSE,Sage Bionetworks,nf1Genotype,,, +Unknown,unknown,,,FALSE,Sage Bionetworks,nf1Genotype,,, +-/-,Homozygous deletion or mutation of NF2.,,,FALSE,Sage Bionetworks,nf2Genotype,,, ++/-,Heterozygous deletion or mutation,,,FALSE,Sage Bionetworks,nf2Genotype,,, ++/+,Homozygous wild type,,,FALSE,Sage Bionetworks,nf2Genotype,,, +Unknown,unknown,,,FALSE,Sage Bionetworks,nf2Genotype,,, +runType,Is the sequencing run single or paired end?,"singleEnd, pairedEnd",,FALSE,Sage Bionetworks,ngs,,, +readPair,The read of origin,"1, 2",,FALSE,,ngs,,, +isStranded,Whether or not the library is stranded. (Note: TRUE = Yes; FALSE = No),"TRUE, FALSE",,FALSE,,ngs,,, +readPairOrientation,The relative orientation of the reads in a paired-end protocol,"inward, outward, matching",,FALSE,,ngs,,, +readStrandOrigin,The strand from which the read originates in a strand-specific protocol,"forward, reverse",,FALSE,,ngs,,, +libraryPrep,The general strategy by which the library was prepared,"rRNAdepletion, polyAselection, lncRNAenrichment, miRNAenrichment",,FALSE,,ngs,,, +libraryPreparationMethod,Method by which library was prepared,"10x, CEL-seq, Drop-Seq, Smart-seq2, TruSeq, Smart-seq4, Omni-ATAC, NEBNext mRNA Library Prep Reagent Set for Illumina, IDT xGen Exome Research Panel",,FALSE,,ngs,,, +nucleicAcidSource,Source of the extracted nucleic acid used in the experiment,"bulk cell, single cell, bulk nuclei, single nucleus, mitochondria",,FALSE,Sage Bionetworks,ngs,,, +dissociationMethod,Procedure by which a biological specimen is dissociated into individual cells or a cell suspension,"10x_v2, FACS, Fluidigm C1, drop-seq, inDrop, mouth pipette, bulk, enzymatic, mechanical, none",,FALSE,https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0009088,ngs,,, +readLength,,,,FALSE,,ngs,,, +bulk cell,All cells from bulk sample,,,FALSE,https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json,nucleicAcidSource,,, +single cell,Single cell,,,FALSE,https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json,nucleicAcidSource,,, +bulk nuclei,All nuclei from bulk sample,,,FALSE,https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json,nucleicAcidSource,,, +single nucleus,Single nuclei,,,FALSE,https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json,nucleicAcidSource,,, +mitochondria,Mitochondria only,,,FALSE,https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json,nucleicAcidSource,,, +lymph node,A bean-shaped organ surrounded by a connective tissue capsule.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C12745,organ,,, +kidney,One of the two bean-shaped organs located on each side of the spine in the retroperitoneum.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C12415,organ,,, +skin,The integument of an animal (as a fur-bearing mammal or a bird) separated from the body usually with its hair or feathers.,,,FALSE,http://purl.obolibrary.org/obo/BTO_0001253,organ,,, +mammary gland,"A specialized accessory gland of the skin of mammals that secretes milk. The gland is typically only developed in females, and regresses in males.",,,FALSE,http://purl.obolibrary.org/obo/UBERON_0001911,organ,,, +nerves,"Any of the filamentous bands of nervous tissue that connect parts of the nervous system with the other organs, conduct nervous impulses, and are made up of axons and dendrites together with protective and supportive structures.",,,FALSE,http://purl.obolibrary.org/obo/BTO_0000925,organ,,, +brain,The portion of the vertebrate central nervous system that constitutes the organ of thought and neural coordination.,,,FALSE,http://purl.obolibrary.org/obo/BTO_0000142,organ,,, +blood,"The fluid that circulates in the heart, arteries, capillaries, and veins of a vertebrate animal carrying nourishment and oxygen to and bringing away waste products from all parts of the body.",,,FALSE,http://purl.obolibrary.org/obo/BTO_0000089,organ,,, +breast,The fore or ventral part of the body between the neck and the abdomen.,,,FALSE,http://purl.obolibrary.org/obo/BTO_0000149,organ,,, +colon,The part of the large intestine that extends from the cecum to the rectum.,,,FALSE,http://purl.obolibrary.org/obo/BTO_0000269,organ,,, +lung,One of the usually paired compound saccular thoracic organs that constitute the basic respiratory organ of air-breathing vertebrates.,,,FALSE,http://purl.obolibrary.org/obo/BTO_0000763,organ,,, +prostate,Lobular organ the parenchyma of which has as its parts glandular acini which are continuous with the prostatic part of the urethra.,,,FALSE,http://purl.obolibrary.org/obo/FMA_9600,organ,,, +pancreas,A large lobulated gland of vertebrates that secretes digestive enzymes and the hormones insulin and glucagon.,,,FALSE,http://purl.obolibrary.org/obo/BTO_0000988,organ,,, +ovary,One of the typically paired essential female reproductive organs that produce eggs and in vertebrates female sex hormones.,,,FALSE,http://purl.obolibrary.org/obo/BTO_0000975,organ,,, +spleen,"A highly vascular ductless organ that is located in the left abdominal region near the stomach or intestine of most vertebrates and is concerned with final destruction of red blood cells, filtration and storage of blood, and production of lymphocytes.",,,FALSE,http://purl.obolibrary.org/obo/BTO_0001281,organ,,, +bone marrow,"The soft, fatty, vascular tissue that fills most bone cavities and is the source of red blood cells and many white blood cells.",,,FALSE,http://purl.obolibrary.org/obo/BTO_0000141,organ,,, +Bursa Of Fabricius,"An epithelial outgrowth of lymphoid tissue in the cloaca of young birds, responsible for B-lymphocyte maturation. It undergoes atrophy and involution at six months of age.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C111141,organ,,, +nose,A structure of special sense serving as an organ of the sense of smell and as an entrance to the respiratory tract.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C12756,organ,,, +Olympus DP80,Dual-Sensor Monochrome and Color Camera,,,FALSE,https://www.olympus-lifescience.com/en/camera/color/dp80/,platform,,, +Orbitrap Fusion Lumos Tribrid,Thermo Scientific Orbitrap Fusion Lumos Tribrid Mass Spectrometer,,,FALSE,https://www.thermofisher.com/us/en/home/industrial/mass-spectrometry/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-systems/orbitrap-lc-ms/orbitrap-tribrid-mass-spectrometers/orbitrap-fusion-lumos-mass-spectrometer.html,platform,,, +Spectramax M Series,A Spectramax M Series Microplate Reader,,,FALSE,https://www.moleculardevices.com/products/microplate-readers/multi-mode-readers/spectramax-m-series-readers,platform,,, +LI-COR Odyssey CLx,A LI-COR Odyssey CLx imaging system,,,FALSE,https://www.licor.com/bio/odyssey-clx/,platform,,, +Q Exative HF,Thermo scientific Q Exative,,,FALSE,http://purl.obolibrary.org/obo/MS_10025223,platform,,, +HiSeq3000,Illumina HiSeq 3000,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL21290,platform,,, +HiSeq2500,Illumina HiSeq 2500,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL16791,platform,,, +HiSeq4000,Illumina HiSeq 4000,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL20301,platform,,, +NextSeq500,Illumina NextSeq 500,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL18573,platform,,, +NextSeq 550,Illumina NextSeq 550,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL21697,platform,,, +NextSeq 1000,Illumina NextSeq 1000,,,FALSE,,platform,,, +NextSeq 2000,Illumina NextSeq 2000,,,FALSE,,platform,,, +HiSeq2000,Illumina HiSeq 2000,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL11154,platform,,, +MiSeq,Illumina MiSeq,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL15520,platform,,, +Zeiss LSM 980,A Zeiss Confocal Microscope,,,FALSE,https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwirj4XuwtXsAhVBrp4KHVZyARIQFjABegQIAhAC&url=https%3A%2F%2Fzeiss.ly%2Flsm980-info&usg=AOvVaw0rD50U0aMwfvt4bdfW0Yjd,platform,,, +Affy5.0,Affymetrix Genome-Wide Human SNP 5.0 Array,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6804,platform,,, +Affy6.0,Affymetrix Genome-Wide Human SNP 6.0 Array,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6801,platform,,, +PacBioRSII,PacBio RS II,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL21311,platform,,, +GAIIx,Illumina Genome Analyzer IIx,,,FALSE,https://support.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/datasheet_genome_analyzeriix.pdf,platform,,, +Illumina_HumanOmni1-Quadv1.0,,,,FALSE,https://www.illumina.com/documents/products/datasheets/datasheet_humanomni1_quad.pdf,platform,,, +Illumina_1M,,,,FALSE,,platform,,, +Illumina_h650,,,,FALSE,,platform,,, +Illumina_Omni2pt5M,,,,FALSE,,platform,,, +Illumina_Omni5M,,,,FALSE,,platform,,, +Illumina MouseWG-6 v2.0 expression beadchip,Whole-genome expression profiling in the mouse,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6887,platform,,, +Perlegen300Karray,,,,FALSE,,platform,,, +Agilent44Karray,,,,FALSE,,platform,,, +IlluminaWholeGenomeDASL,Illumina Human Whole-Genome DASL HT,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL13369,platform,,, +IlluminaHumanHap300,,,,FALSE,,platform,,, +NanostringnCounter,,,,FALSE,,platform,,, +LTQ Orbitrap XL,LTQ Orbitrap XL Hybrid Ion Trap-Orbitrap Mass Spectrometer,,,FALSE,https://www.thermofisher.com/order/catalog/product/IQLAAEGAAPFADBMAOK,platform,,, +IlluminaHumanMethylation450,Illumina HumanMethylation450 BeadChip,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL13534,platform,,, +Illumina Infinium MethylationEPIC BeadChip,"An Illumina methylation BeadChip which is an array that interrogates ~ 850,000 methylation sites per sample at single-nucleotide resolution.",,,FALSE,http://purl.obolibrary.org/obo/OBI_0002131,platform,,, +AffymetrixU133AB,,,,FALSE,,platform,,, +Affymetrix Human Gene 1.0 ST Array,Affymetrix Human Gene 1.0 ST Array [transcript (gene) version] in situ oligonucleotide,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6244,platform,,, +AffymetrixU133Plus2,Affymetrix Human Genome U133 Plus 2.0 Array,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL570,platform,,, +HiSeqX,Illumina HiSeq X Platform for whole-genome sequencing,,,FALSE,https://www.illumina.com/systems/sequencing-platforms/hiseq-x.html,platform,,, +Bionano Irys,Performs whole genome mapping in a nanoscale fluidic environment enabling the structure of the genome to be imaged and then analyzed at the single molecule level,,,FALSE,https://bionanogenomics.com/products/irys/,platform,,, +Infinium HumanOmniExpressExome,Infinium HumanOmniExpressExome BeadChip,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL18224,platform,,, +Illumina_NovaSeq_6000,Illumina NovaSeq 6000 performs whole-genome sequencing,,,FALSE,https://www.illumina.com/systems/sequencing-platforms/novaseq.html,platform,,, +cell lysate,a cell lysate is a material entity which is output of a cell lysis process,,,TRUE,http://purl.obolibrary.org/obo/OBI_1000036,proteinExtractSource,,, +nuclear extract,Nuclear extracts contain proteins in nuclear compartment of the cell,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C19832,proteinExtractSource,,, +mitochondria,Mitochondria only,,,FALSE,https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json,proteinExtractSource,,, +cytoplasm,That portion of the cell contained within the plasma membrane but excluding the nucleus.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C13226,proteinExtractSource,,, +1,One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert.,,,FALSE,http://purl.obolibrary.org/obo/SO_0000007,readPair,,, +2,One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert.,,,FALSE,http://purl.obolibrary.org/obo/SO_0000007,readPair,,, +inward,Reads face each other,,,FALSE,Sage Bionetworks,readPairOrientation,,, +outward,Reads face away from each other,,,FALSE,Sage Bionetworks,readPairOrientation,,, +matching,Reads face the same direction,,,FALSE,Sage Bionetworks,readPairOrientation,,, +forward,Read 1 (or unpaired read) comes from the forward strand and read 2 (if applicable) comes from the reverse strand; equivalent to Tophat 'fr-secondstrand' type,,,FALSE,Sage Bionetworks,readStrandOrigin,,, +reverse,read 1 (or unpaired read) comes from the reverse strand and read 2 (if applicable) comes from the forward strand; equivalent to Tophat 'fr-firststrand' type,,,FALSE,Sage Bionetworks,readStrandOrigin,,, +GRCh38,Genome Reference Consortium Human Build 38,,,FALSE,https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26,referenceSet,,, +GRCh37,Genome Reference Consortium Human Build 37,,,FALSE,https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13/,referenceSet,,, +MMUL1.0,Ensembl preliminary assembly Macaca mulatta,,,FALSE,https://jul2016.archive.ensembl.org/Macaca_mulatta/Info/Index,referenceSet,,, +HRC,Human haplotype reference panel,,,FALSE,http://www.haplotype-reference-consortium.org,referenceSet,,, +experimentalData,"Any file derived from or pertaining to a scientific experiment. experimentalData annotations should be applied, possibly disease-related",,"dataType,dataSubtype,specimenID,individualID,species, diagnosis,isCellLine,sex,tissue,tumorType,nf1Genotype,nf2Genotype,genePerturbationType,genePerturbed,experimentalCondition,experimentalTimepoint,timePointUnit",FALSE,Sage Bionetworks,resourceType,,, +result,"Any file that reports data results. Examples include figures, presentations, analysis, etc.",,,FALSE,Sage Bionetworks,resourceType,,, +tool,"Any file or link that represents a tool, model, or algorithm; the tool annotations could be applied",,,FALSE,Sage Bionetworks,resourceType,,, +report,"a document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record).",,,FALSE,http://purl.obolibrary.org/obo/IAO_0000088,resourceType,,, +singleEnd,A library preparation that results in the creation of a library of 5' ends of DNA.,,,FALSE,Sage Bionetworks,runType,,, +pairedEnd,A library preparation that results in the creation of a library of the 5' and 3' ends of DNA or cDNA fragments using adaptors and endonucleases. The preparation may or may not include cloning process.,,,FALSE,http://purl.obolibrary.org/obo/OBI_0001852,runType,,, +experimentalCondition,A free-text description of the experimental condition (e.g. 5 mM doxorubicin). ,,,FALSE,Sage Bionetworks,sageCommunity,,, +experimentalTimepoint,The numeric value indicating the time elapsed from the beginning of the experiment at which the specimen was collected. Use in tandem with timePointUnit,,,FALSE,Sage Bionetworks,sageCommunity,,, +genePerturbed,The HUGO gene symbol for the gene that is perturbed. ,,,FALSE,Sage Bionetworks,sageCommunity,,, +resourceType,The type of resource being stored and annotated,"experimentalData, curatedData, result, tool, report",,TRUE,,sageCommunity,,, +fileFormat,"Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software","bash script,bedgraph,ai,idx,idat,bam,bai,excel,powerpoint,tif,png,doc,pdf,hdf,fasta,fastq,sam,vcf,bcf,maf,bed,chp,cel,sif,tsv,csv,txt,plink,bigwig,wiggle,gct,bgzip,zip,seg,html,mov,hyperlink,svs,md,flagstat,gtf,raw,msf,rmd,bed narrowPeak,bed broadPeak,bed gappedPeak,avi,pzfx,fig,xml,tar,R script,abf,bpm,dat,jpg,locs,Sentrix descriptor file,Python script,sav,gzip,sdf,RData,hic,ab1,7z,gff3,json,sqlite,svg,sra,recal,tranches,mtx,tagAlign,dup,DICOM,czi,mzML,SPAR,SDAT,nii,PAR,REC,hdr,img,sf",,TRUE,,sageCommunity,,, +Homo sapiens,Homo sapiens with taxonomy ID: 9606 and Genbank common name: human,,,FALSE,https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606&lvl=3&lin=f&keep=1&srchmode=1&unlock,species,,, +Mus musculus,Mus musculus with taxonomy ID: 10090 and Genbank common name: house mouse,,modelSystemName,FALSE,https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=10090&lvl=3&lin=f&keep=1&srchmode=1&unlock,species,,, +Mus musculus (humanized),Mus musculus with taxonomy ID: 10090 and Genbank common name: house mouse,,modelSystemName,FALSE,https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=10090&lvl=3&lin=f&keep=1&srchmode=1&unlock,species,,, +Rattus norvegicus,Rattus with taxonomy ID:10116 and Genbank common name: Norway rat,,modelSystemName,FALSE,https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=10116&lvl=3&lin=f&keep=1&srchmode=1&unlock,species,,, +Drosophila melanogaster,Drosophila melanogaster with taxonomy ID: 7227 and Genbank common name: fruit fly,,modelSystemName,FALSE,https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=7227&lvl=3&p=has_linkout&p=blast_url&p=genome_blast&p=mapview&lin=f&keep=1&srchmode=1&unlock,species,,, +Rhesus macaque,Macaca mulatta with taxonomy ID: 9544 and Genbank common name: Rhesus monkey,,,FALSE,https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9544&lvl=3&p=has_linkout&p=blast_url&p=genome_blast&p=mapview&lin=f&keep=1&srchmode=1&unlock,species,,, +Pan troglodytes,Pan troglodytes with taxonomy ID: 9598 and Genbank common name: chimpanzee,,,FALSE,https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9598&lvl=3&lin=f&keep=1&srchmode=1&unlock,species,,, +Gallus gallus,"The common domestic fowl, Chicken.",,,FALSE,https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9031,species,,, +Sus scrofa,Sus scrofa with taxonomy ID: 9823 and Genbank common name: pig,,modelSystemName,FALSE,https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9823,species,,, +Oryctolagus cuniculus," +Oryctolagus cuniculus with taxonomy ID: 9986 and Genbank common name: rabbit",,modelSystemName,FALSE,https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9986&lvl=3&lin=f&keep=1&srchmode=1&unlock,species,,, +Danio rerio,Danio rerio with taxonomy ID: 7955 and Genbank common name: zebrafish,,modelSystemName,FALSE,https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=7955&lvl=3&lin=f&keep=1&srchmode=1&unlock,species,,, +seconds,,,,FALSE,,timePointUnit,,, +minutes,,,,FALSE,,timePointUnit,,, +hours,,,,FALSE,,timePointUnit,,, +days,,,,FALSE,,timePointUnit,,, +weeks,,,,FALSE,,timePointUnit,,, +months,,,,FALSE,,timePointUnit,,, +nerve tissue,"Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature.",,,FALSE,https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0003714,tissue,,, +optic nerve,The nerve that carries messages from the retina to the brain.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C12761,tissue,,, +serum,Liquid derived from blood plasma that has clotting factors removed.,,,FALSE,https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0001977,tissue,,, +plasma,"Plasma is the fluid (noncellular) portion of the circulating blood, as distinguished from the serum that is the fluid portion of the blood obtained by removal of the fibrin clot and blood cells after coagulation.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C13356,tissue,,, +splenocyte,Any leukocyte that is part of a spleen.,,,FALSE,https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_2000074,tissue,,, +blood,A fluid that is composed of blood plasma and erythrocytes.,,,FALSE,https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0000178,tissue,,, +primary tumor,"A primary tumor is the tumor at the initial site of cancer, not where the cancer may have spread or metastasized, called the secondary tumor.",,tumorType,FALSE,https://cancergenome.nih.gov/cancersselected/biospeccriteria,tissue,,, +embryonic tissue,A portion of tissue that is part of an embryo.,,,FALSE,http://purl.obolibrary.org/obo/UBERON_0005291,tissue,,, +meninges,The three thin layers of tissue that cover and protect the brain and spinal cord.,,,FALSE,https://www.ncbi.nlm.nih.gov/pubmedhealth/PMHT0024758/,tissue,,, +bone marrow,"The soft, fatty, vascular tissue that fills most bone cavities and is the source of red blood cells and many white blood cells.",,,FALSE,http://purl.obolibrary.org/obo/BTO_0000141,tissue,,, +Buccal Mucosa,"The mucosal membranes located on the inside of the cheek, in the buccal cavity.The inner lining of the cheeks.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C12505,tissue,,, +Dorsal Root Ganglion,Ganglion with sensory function within the vertebral column.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C12462,tissue,,, +cerebral cortex,"The outer layer of the cerebrum composed of neurons and unmyelinated nerve fibers. It is responsible for memory, attention, consciousness and other higher levels of mental function.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C12443,tissue,,, +sciatic nerve,"The longest single nerve that is formed by the merging of the ventral rami of the L4, L5, and S1 in the pelvis and passes down the lower limb where it divides into the common peroneal and tibial nerves",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C52810,tissue,,, +unspecified,Unspecified tissue or tissues from an organ.,,,FALSE,Sage Bionetworks,tissue,,, +whole brain,Brain tissue not limited to a specific region.,,,FALSE,Sage Bionetworks,tissue,,, +Buffy Coat,The middle layer of an anticoagulated blood specimen following separation by centrifugation. It contains most of the white blood cells and platelets.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C84507,tissue,,, +Human,,,,FALSE,,transplantationRecipientSpecies,,, +Mouse,,,,FALSE,,transplantationRecipientSpecies,,, +allograft,"Tissues, cells, or organs transplanted between genetically different individuals of the same species",,,FALSE,https://www.ncbi.nlm.nih.gov/mesh/68064591,transplantationType,,, +xenograft,"Tissues, cells or organs transplanted between animals of different species",,"transplantationRecipientSpecies,transplantationRecipientTissue",FALSE,https://www.ncbi.nlm.nih.gov/mesh/68064593,transplantationType,,, +autograft,"Transplant comprised of an individual's own tissue, transferred from one part of the body to another.",,"transplantationRecipientSpecies,transplantationRecipientTissue",FALSE,https://www.ncbi.nlm.nih.gov/mesh/68064592,transplantationType,,, +isograft,"Tissues, cells or organs transplanted between genetically identical individuals",,,FALSE,https://www.ncbi.nlm.nih.gov/mesh/68064596,transplantationType,,, +teratoma,"A non-seminomatous germ cell tumor characterized by the presence of various tissues which correspond to the different germinal layers (endoderm, mesoderm, and ectoderm). It occurs in the testis, ovary, and extragonadal sites including central nervous system, mediastinum, lung, and stomach",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C3403,tumorType,,, +Cutaneous Neurofibroma,A neurofibroma that grows along small branches of nerves in the dermis in patients with neurofibromatosis. It presents as a solid cutaneous tumor.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C128451,tumorType,,, +Plexiform Neurofibroma,"An elongated and multinodular neurofibroma, formed when the tumor involves either multiple trunks of a plexus or multiple fascicles of a large nerve, such as the sciatic. Some plexiform neurofibromas resemble a bag of worms, others produce a massive ropy enlargement of the nerve.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C3797,tumorType,,, +Atypical Neurofibroma,A neurofibroma characterized by the presence of cellular pleomorphism.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C41426,tumorType,,, +Malignant Peripheral Nerve Sheath Tumor,"The tumors usually develop along peripheral or cranial nerves and are a central feature of NEUROFIBROMATOSIS 1, where they may occur intracranially or involve spinal roots.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C3798,tumorType,,, +Adenocarcinoma,"A common cancer characterized by the presence of malignant glandular cells. Morphologically, adenocarcinomas are classified according to the growth pattern (e.g., papillary, alveolar) or according to the secreting product (e.g., mucinous, serous).",,,FALSE,https://www.ebi.ac.uk/ols/ontologies/mp/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCIT_C2852,tumorType,,, +Carcinoma,A cell type cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells.,,,FALSE,https://www.ebi.ac.uk/ols/ontologies/doid/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_305,tumorType,,, +Ductal Carcinoma,"Invasive ductal carcinoma (IDC), an infiltrating, malignant and abnormal proliferation of neoplastic cells in the breast tissue, or ductal carcinoma in situ (DCIS), a noninvasive, possibly malignant, neoplasm that is still confined to the milk ducts (lactiferous ducts), where breast cancer most often originates.",,,FALSE,https://www.ebi.ac.uk/ols/ontologies/bto/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBTO_0004851,tumorType,,, +Melanoma,"A malignant, usually aggressive tumor composed of atypical, neoplastic melanocytes.",,,FALSE,https://www.ebi.ac.uk/ols/ontologies/mp/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCIT_C3224,tumorType,,, +Glioma,"A benign or malignant brain and spinal cord tumor that arises from glial cells (astrocytes, oligodendrocytes, ependymal cells). Tumors that arise from astrocytes are called astrocytic tumors or astrocytomas. Tumors that arise from oligodendrocytes are called oligodendroglial tumors. Tumors that arise from ependymal cells are called ependymomas.",,,FALSE,http://purl.obolibrary.org/obo/MONDO_0021042,tumorType,,, +Low Grade Glioma,Low grade gliomas are brain tumors that come from two different types of brain cells known as astrocytes and oligodendrocytes.,,,FALSE,https://www.urmc.rochester.edu/neurosurgery/specialties/neurooncology/conditions/low-grade-glioma.aspx,tumorType,,, +Diffuse Astrocytoma,Also called Low-Grade or Astrocytoma Grade II is a subtype of glial tumor of the brain or spinal cord showing astrocytic differentiation.,,,FALSE,https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0000272,tumorType,,, +Anaplastic Astrocytoma,"A diffusely infiltrating, WHO grade III astrocytoma with focal or dispersed anaplasia, and a marked proliferative potential. It may arise from a low-grade astrocytoma, but it can also be diagnosed at first biopsy, without indication of a less malignant precursor lesion. It has an intrinsic tendency for malignant progression to glioblastoma.",,,FALSE,https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0002499,tumorType,,, +Glioblastoma,"Develop primarily through increasing anaplasia of well differentiated gliomas, mainly astrocytomas or oligodendrogliomas. Typically large and contain cells of different sizes with irrregular nuclei and atypical mitotic figures.",,,FALSE,https://www.ebi.ac.uk/ols/ontologies/mpath/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMPATH_564,tumorType,,, +Schwannoma,"A neoplasm that arises from SCHWANN CELLS of the cranial, peripheral, and autonomic nerves. ",,,FALSE,https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0000693,tumorType,,, +Lymphoblastic Lymphoma,A lymphoma composed of immature small to medium-sized precursor lymphoid cells (lymphoblasts). It includes the B- and T-cell lymphoblastic lymphoma.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C9360,tumorType,,, +Meningioma,A generally slow growing tumor attached to the dura mater. It is composed of neoplastic meningothelial (arachnoidal) cells.,,,FALSE,https://www.ebi.ac.uk/ols/ontologies/mp/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCIT_C3230,tumorType,,, +Myeloma,"A bone marrow cancer that is formed of any one of the bone marrow cells belonging to the granulocytic (neutrophil, eosinophil, basophil), monocytic/macrophage, erythroid, megakaryocytic and mast cell lineages.",,,FALSE,http://purl.obolibrary.org/obo/DOID_0070004,tumorType,,, +T Acute Lymphoblastic Leukemia,Acute lymphoblastic leukemia of T-cell origin. It comprises about 15% of childhood cases and 25% of adult cases.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C3183,tumorType,,, +chronic lymphocytic leukemia,A lymphoblastic leukemia characterized by over production of B-cells and their accumulation in bone marrow and blood.,,,FALSE,http://purl.obolibrary.org/obo/DOID_1040,tumorType,,, +Acute Myeloid Leukemia,"A clonal expansion of myeloid blasts in the bone marrow, blood or other tissues.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C3171,tumorType,,, +Not Applicable,,,,FALSE,Sage Bionetworks,tumorType,,, +PacBio Sequel IIe System,PacBio Sequel IIe System,,,,,,,, +PacBio Sequel II System,PacBio Sequel II System,,,,,,,, +NanostringGeoMx,,,,,,,,, +NF,,,"fileFormat, resourceType",TRUE,,,,, +cancer,,,,FALSE,,,,, +neuro,,,,FALSE,,,,, +neurofibromatosis,,,,FALSE,,,,, +compoundScreen,,,,FALSE,,,,, +array,,,,FALSE,,,,, +sageCommunity,,,,FALSE,,,,, +ngs,next gen sequencing/genomics attributes.,"runType,readPair,isStranded,readPairOrientation,readStrandOrigin,libraryPrep,libraryPreparationMethod,libraryPreparationMethod,dissociationMethod,readLength,nucleicAcidSource",,FALSE,,,,, +progressReportNumber,"Indicates which milestone you're annotating data files for. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ""progress report"" timeline. An example: if submitting data for your 6-month milestone report for NTAP, progressReportNumber=1. Also if you are submitting data associated with your first milestone, progressReportNumber =1","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",,FALSE,,template,,, +pdxGenomicsAssay,Extends genomicsAssay for PDX experiments,,"Filename,progressReportNumber,fileFormat,resourceType,dataType,dataSubtype,assay,individualID,sex,species,transplantationRecipientSpecies,transplantationRecipientTissue,transplantationType,modelSystemName,genePerturbationType,genePerturbationTechnology,genePerturbed,diagnosis,specimenID,bodyPart,tissue,nf1Genotype,nf2Genotype,isCellLine,tumorType,specimenPreparationMethod,experimentalCondition,experimentalTimepoint,timePointUnit,platform,runType,readPair,isStranded,readPairOrientation,readStrandOrigin,libraryPrep,libraryPreparationMethod,dissociationMethod,nucleicAcidSource,readLength,readDepth,comments",FALSE,,template,,, +specimenPreparationMethod,Term that represents the method used to preserve the sample before preparing the sample for sequencing,"Fresh collected, Flash frozen, FFPE, Cryopreserved, OCT, RNAlater, formalin-fixed, ethanol, Viably frozen",,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=sample&anchor=preservation_method,ngs,,, +Single Cell RNA Sequencing,A procedure that can determine the nucleotide sequence for all of the RNA transcripts in an amplified nucleotide sample that was derived from a single cell.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C171152,assay,,, +updateMilestoneReport,Defines a metadata template for updating milestone report values in NF studies -- currently a supported feature for NTAP and GFF.,,"Filename,progressReportNumber",TRUE,,template,,, +template,Parent attribute for the manifest template attributes. ,,,,,,,, +normal,No pathological entity observable.,,,FALSE,http://purl.obolibrary.org/obo/MPATH_458,,,, +comments,Brief free-text comments that may also be important to understanding the data. ,,,FALSE,Sage Bionetworks,experimentalData,,, +Massive Soft Tissue Neurofibroma,,,,FALSE,,tumorType,,, +Diffuse Infiltrating Neurofibroma,,,,FALSE,,tumorType,,, +Localized Neurofibroma,,,,FALSE,,tumorType,,, +Neurofibroma with Degenerative Atypia,,,,FALSE,,tumorType,,, +Neurofibroma,,,,,,tumorType,,, +mesentery,,,,FALSE,,organ,,, +connective tissue,,,,FALSE,,tissue,,, +Viably frozen,,,,FALSE,,specimenPreparationMethod,,, +scalp,,,,FALSE,,bodyPart,,, +pelvis,,,,FALSE,,bodyPart,,, +neck,,,,FALSE,,bodyPart,,, +leg,,,,FALSE,,bodyPart,,, +liver,,,,FALSE,,organ,,, +axilla,,,,FALSE,,bodyPart,,, +acetabulum,,,,FALSE,,bodyPart,,, +forearm,,,,FALSE,,bodyPart,,, +muscle,,,,FALSE,,bodyPart,,, +finger,,,,FALSE,,bodyPart,,, +thoracic spine,,,,FALSE,http://purl.obolibrary.org/obo/UBERON_0006073,bodyPart,,, +groin,Anatomically also known as the inguinal part of abdomen.,,,FALSE,http://purl.obolibrary.org/obo/UBERON_0008337,bodyPart,,, +back,Anatomically also known as the dorsum.,,,FALSE,http://purl.obolibrary.org/obo/UBERON_0001137,bodyPart,,, +iliac spine,,,,FALSE,http://purl.obolibrary.org/obo/UBERON_0013707,bodyPart,,, +spine,,,,FALSE,http://purl.obolibrary.org/obo/UBERON_0001130,bodyPart,,, +shoulder,,,,FALSE,,bodyPart,,, +scapula,,,,FALSE,,bodyPart,,, +curatedData,"Any file derived from or pertaining a manually or programatically curated data resource. Examples include: reference sequences, drug information databases, identifier maps""",,,FALSE,,,,, +transplantationRecipientTissue,Tissue into which a xenograph sample is transplanted,,,FALSE,,,,, +tumor-adjacent normal,Tissue comprised of morphologically normal tissue collected from the area immediately surrounding a tumor.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C164032,tissue,,, +PDX tissue,Patient derived xenograft tissue,,,FALSE,,tissue,,, +CDX tissue,Cell line derived xenograft tissue,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C156443,tissue,,, +tumor,"General term for tumor sample – use when it is unknown when a more specific clinical classification is unknown, e.g. whether it is primary or secondary.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C18009,tissue,,, +metastatic tumor,"For neoplasms, a non-infiltrating and non-metastasizing neoplastic process that is characterized by the absence of morphologic features associated with malignancy (e.g., severe atypia, nuclear pleomorphism, tumor cell necrosis, and abnormal mitoses).",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C14172,tissue,,, +metastatic/recurrent tumor,A tumor with metastatic/recurrent characteristic.,,,FALSE,,tissue,,, +recurrent tumor,A tumor described with recurrent characteristic.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C4798,tissue,,, diff --git a/NF.jsonld b/NF.jsonld index 19dca232..0960cc18 100644 --- a/NF.jsonld +++ b/NF.jsonld @@ -2932,125 +2932,6 @@ "sms:required": "sms:false", "sms:validationRules": [] }, - { - "@id": "bts:Noveltyresponsebehavior", - "@type": "rdfs:Class", - "rdfs:comment": "Behavior related to the exploration/investigation of a novel object, situation or environment.", - "rdfs:label": "Noveltyresponsebehavior", - "rdfs:subClassOf": [ - { - "@id": "bts:Assay" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "novelty response behavior", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Activeavoidancelearningbehavior", - "@type": "rdfs:Class", - "rdfs:comment": "Avoidance learning when the action occurs.", - "rdfs:label": "Activeavoidancelearningbehavior", - "rdfs:subClassOf": [ - { - "@id": "bts:Assay" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "active avoidance learning behavior", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Contextualconditioningbehavior", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Contextualconditioningbehavior", - "rdfs:subClassOf": [ - { - "@id": "bts:Assay" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "contextual conditioning behavior", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Anxiety-relatedbehavior", - "@type": "rdfs:Class", - "rdfs:comment": "An emotional behavior related to a feeling of uneasiness or nervousness triggered by an identifiable triggering stimulus.", - "rdfs:label": "Anxiety-relatedbehavior", - "rdfs:subClassOf": [ - { - "@id": "bts:Assay" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "anxiety-related behavior", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Memorybehavior", - "@type": "rdfs:Class", - "rdfs:comment": "Behavior related with the ability of an organism's ability to store, retain, and recall information and experiences.", - "rdfs:label": "Memorybehavior", - "rdfs:subClassOf": [ - { - "@id": "bts:Assay" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "memory behavior", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Kinestheticbehavior", - "@type": "rdfs:Class", - "rdfs:comment": "Movement behavior of the body or its parts.", - "rdfs:label": "Kinestheticbehavior", - "rdfs:subClassOf": [ - { - "@id": "bts:Assay" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "kinesthetic behavior", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Locomotoractivationbehavior", - "@type": "rdfs:Class", - "rdfs:comment": "Activation of locomotory behavior.", - "rdfs:label": "Locomotoractivationbehavior", - "rdfs:subClassOf": [ - { - "@id": "bts:Assay" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "locomotor activation behavior", - "sms:required": "sms:false", - "sms:validationRules": [] - }, { "@id": "bts:OxBS-Seq", "@type": "rdfs:Class", @@ -3615,7 +3496,19 @@ "@id": "bts:Teratoma" }, { - "@id": "bts:NotApplicable" + "@id": "bts:MassiveSoftTissueNeurofibroma" + }, + { + "@id": "bts:DiffuseInfiltratingNeurofibroma" + }, + { + "@id": "bts:LocalizedNeurofibroma" + }, + { + "@id": "bts:Neurofibroma" + }, + { + "@id": "bts:NeurofibromawithDegenerativeAtypia" } ], "sms:displayName": "tumorType", @@ -3644,6 +3537,9 @@ }, { "@id": "bts:Knockout" + }, + { + "@id": "bts:NotApplicable" } ], "sms:displayName": "genePerturbationType", @@ -5557,27 +5453,6 @@ { "@id": "bts:DNAopticalmapping" }, - { - "@id": "bts:Noveltyresponsebehavior" - }, - { - "@id": "bts:Activeavoidancelearningbehavior" - }, - { - "@id": "bts:Contextualconditioningbehavior" - }, - { - "@id": "bts:Anxiety-relatedbehavior" - }, - { - "@id": "bts:Memorybehavior" - }, - { - "@id": "bts:Kinestheticbehavior" - }, - { - "@id": "bts:Locomotoractivationbehavior" - }, { "@id": "bts:OxBS-Seq" }, @@ -5717,7 +5592,7 @@ { "@id": "bts:BodyPart", "@type": "rdfs:Class", - "rdfs:comment": "Named areas of the body.", + "rdfs:comment": "Sample location referring to a named area of the body, inclusive of gross anatomical structures and organ parts. ", "rdfs:label": "BodyPart", "rdfs:subClassOf": [ { @@ -5730,6 +5605,111 @@ "schema:rangeIncludes": [ { "@id": "bts:Head" + }, + { + "@id": "bts:Neck" + }, + { + "@id": "bts:Scalp" + }, + { + "@id": "bts:Leg" + }, + { + "@id": "bts:Pelvis" + }, + { + "@id": "bts:Mesentery" + }, + { + "@id": "bts:Axilla" + }, + { + "@id": "bts:Acetabulum" + }, + { + "@id": "bts:Forearm" + }, + { + "@id": "bts:Muscle" + }, + { + "@id": "bts:Finger" + }, + { + "@id": "bts:Thoracicspine" + }, + { + "@id": "bts:Groin" + }, + { + "@id": "bts:Back" + }, + { + "@id": "bts:Iliacspine" + }, + { + "@id": "bts:Spine" + }, + { + "@id": "bts:Shoulder" + }, + { + "@id": "bts:Scapula" + }, + { + "@id": "bts:Lymphnode" + }, + { + "@id": "bts:Kidney" + }, + { + "@id": "bts:Skin" + }, + { + "@id": "bts:Mammarygland" + }, + { + "@id": "bts:Nerves" + }, + { + "@id": "bts:Brain" + }, + { + "@id": "bts:Blood" + }, + { + "@id": "bts:Breast" + }, + { + "@id": "bts:Colon" + }, + { + "@id": "bts:Lung" + }, + { + "@id": "bts:Liver" + }, + { + "@id": "bts:Prostate" + }, + { + "@id": "bts:Pancreas" + }, + { + "@id": "bts:Ovary" + }, + { + "@id": "bts:Spleen" + }, + { + "@id": "bts:Bonemarrow" + }, + { + "@id": "bts:BursaOfFabricius" + }, + { + "@id": "bts:Nose" } ], "sms:displayName": "bodyPart", @@ -5780,6 +5760,9 @@ { "@id": "bts:Lung" }, + { + "@id": "bts:Liver" + }, { "@id": "bts:Prostate" }, @@ -5972,6 +5955,27 @@ }, { "@id": "bts:Sciaticnerve" + }, + { + "@id": "bts:Connectivetissue" + }, + { + "@id": "bts:Tumor-adjacentnormal" + }, + { + "@id": "bts:PDXtissue" + }, + { + "@id": "bts:CDXtissue" + }, + { + "@id": "bts:Metastatic/recurrenttumor" + }, + { + "@id": "bts:Recurrenttumor" + }, + { + "@id": "bts:Metastatictumor" } ], "sms:displayName": "tissue", @@ -6114,6 +6118,9 @@ }, { "@id": "bts:OrbitrapFusionLumosTribrid" + }, + { + "@id": "bts:IlluminaNovaSeq6000" } ], "sms:displayName": "platform", @@ -8491,6 +8498,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:IDTxGenExomeResearchPanel", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "IDTxGenExomeResearchPanel", + "rdfs:subClassOf": [ + { + "@id": "bts:LibraryPreparationMethod" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "IDT xGen Exome Research Panel", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:Individual", "@type": "rdfs:Class", @@ -10903,7 +10927,7 @@ { "@id": "bts:Unknown", "@type": "rdfs:Class", - "rdfs:comment": "TBD", + "rdfs:comment": "unknown", "rdfs:label": "Unknown", "rdfs:subClassOf": [ { @@ -10971,7 +10995,7 @@ { "@id": "bts:Unknown", "@type": "rdfs:Class", - "rdfs:comment": "TBD", + "rdfs:comment": "unknown", "rdfs:label": "Unknown", "rdfs:subClassOf": [ { @@ -11181,6 +11205,9 @@ }, { "@id": "bts:NEBNextmRNALibraryPrepReagentSetforIllumina" + }, + { + "@id": "bts:IDTxGenExomeResearchPanel" } ], "sms:displayName": "libraryPreparationMethod", @@ -12324,6 +12351,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:IlluminaNovaSeq6000", + "@type": "rdfs:Class", + "rdfs:comment": "Illumina NovaSeq 6000 performs whole-genome sequencing", + "rdfs:label": "IlluminaNovaSeq6000", + "rdfs:subClassOf": [ + { + "@id": "bts:Platform" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Illumina_NovaSeq_6000", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:Celllysate", "@type": "rdfs:Class", @@ -12650,24 +12694,7 @@ "sms:validationRules": [] }, { - "@id": "bts:CuratedData", - "@type": "rdfs:Class", - "rdfs:comment": "Any file derived from or pertaining a manually or programatically curated data resource. Examples include: reference sequences, drug information databases, identifier maps", - "rdfs:label": "CuratedData", - "rdfs:subClassOf": [ - { - "@id": "bts:ResourceType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "curatedData", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Result", + "@id": "bts:Result", "@type": "rdfs:Class", "rdfs:comment": "Any file that reports data results. Examples include figures, presentations, analysis, etc.", "rdfs:label": "Result", @@ -14373,23 +14400,6 @@ "sms:required": "sms:false", "sms:validationRules": [] }, - { - "@id": "bts:CuratedData", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "CuratedData", - "rdfs:subClassOf": [ - { - "@id": "schema:Thing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "curatedData", - "sms:required": "sms:false", - "sms:validationRules": [] - }, { "@id": "bts:Array", "@type": "rdfs:Class", @@ -14483,7 +14493,7 @@ "rdfs:label": "ProgressReportNumber", "rdfs:subClassOf": [ { - "@id": "bts:NF" + "@id": "bts:Template" } ], "schema:isPartOf": { @@ -14519,6 +14529,9 @@ }, { "@id": "bts:10" + }, + { + "@id": "bts:NotApplicable" } ], "sms:displayName": "progressReportNumber", @@ -14528,11 +14541,11 @@ { "@id": "bts:PdxGenomicsAssay", "@type": "rdfs:Class", - "rdfs:comment": "TBD", + "rdfs:comment": "Extends genomicsAssay for PDX experiments", "rdfs:label": "PdxGenomicsAssay", "rdfs:subClassOf": [ { - "@id": "bts:NF" + "@id": "bts:Template" } ], "schema:isPartOf": { @@ -14574,6 +14587,9 @@ { "@id": "bts:TransplantationRecipientSpecies" }, + { + "@id": "bts:TransplantationRecipientTissue" + }, { "@id": "bts:TransplantationType" }, @@ -14596,7 +14612,7 @@ "@id": "bts:SpecimenID" }, { - "@id": "bts:Organ" + "@id": "bts:BodyPart" }, { "@id": "bts:Tissue" @@ -14670,7 +14686,7 @@ { "@id": "bts:SpecimenPreparationMethod", "@type": "rdfs:Class", - "rdfs:comment": "Term that represents the method used to preserve the sample before preparing the sample for seqencing", + "rdfs:comment": "Term that represents the method used to preserve the sample before preparing the sample for sequencing", "rdfs:label": "SpecimenPreparationMethod", "rdfs:subClassOf": [ { @@ -14704,6 +14720,9 @@ }, { "@id": "bts:Ethanol" + }, + { + "@id": "bts:Viablyfrozen" } ], "sms:displayName": "specimenPreparationMethod", @@ -14804,206 +14823,767 @@ "sms:validationRules": [] }, { - "@id": "bts:TRUE", + "@id": "bts:MassiveSoftTissueNeurofibroma", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "TRUE", + "rdfs:label": "MassiveSoftTissueNeurofibroma", "rdfs:subClassOf": [ { - "@id": "bts:IsCellLine" + "@id": "bts:TumorType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "TRUE", + "sms:displayName": "Massive Soft Tissue Neurofibroma", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FALSE", + "@id": "bts:DiffuseInfiltratingNeurofibroma", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "FALSE", + "rdfs:label": "DiffuseInfiltratingNeurofibroma", "rdfs:subClassOf": [ { - "@id": "bts:IsCellLine" + "@id": "bts:TumorType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "FALSE", + "sms:displayName": "Diffuse Infiltrating Neurofibroma", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Nuclei", + "@id": "bts:LocalizedNeurofibroma", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Nuclei", + "rdfs:label": "LocalizedNeurofibroma", "rdfs:subClassOf": [ { - "@id": "bts:ProteinExtractSource" + "@id": "bts:TumorType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "nuclei", + "sms:displayName": "Localized Neurofibroma", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ChIPseq", + "@id": "bts:NeurofibromawithDegenerativeAtypia", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "ChIPseq", + "rdfs:label": "NeurofibromawithDegenerativeAtypia", "rdfs:subClassOf": [ { - "@id": "bts:ImmunoAssayType" + "@id": "bts:TumorType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "ChIPseq", + "sms:displayName": "Neurofibroma with Degenerative Atypia", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ATAC-seq", + "@id": "bts:Neurofibroma", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "ATAC-seq", + "rdfs:label": "Neurofibroma", "rdfs:subClassOf": [ { - "@id": "bts:ImmunoAssayType" + "@id": "bts:TumorType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "ATAC-seq", + "sms:displayName": "Neurofibroma", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:+/?", + "@id": "bts:Mesentery", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "+/?", + "rdfs:label": "Mesentery", "rdfs:subClassOf": [ { - "@id": "bts:Nf2Genotype" + "@id": "bts:Organ" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "+/?", + "sms:displayName": "mesentery", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:-/?", + "@id": "bts:Connectivetissue", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "-/?", + "rdfs:label": "Connectivetissue", "rdfs:subClassOf": [ { - "@id": "bts:Nf2Genotype" + "@id": "bts:Tissue" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "-/?", + "sms:displayName": "connective tissue", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ModelSystemStrainNomenclature", + "@id": "bts:Viablyfrozen", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "ModelSystemStrainNomenclature", + "rdfs:label": "Viablyfrozen", "rdfs:subClassOf": [ { - "@id": "bts:GenomicsAssay" + "@id": "bts:SpecimenPreparationMethod" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "modelSystemStrainNomenclature", + "sms:displayName": "Viably frozen", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ReadDepth", + "@id": "bts:Scalp", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "ReadDepth", + "rdfs:label": "Scalp", "rdfs:subClassOf": [ { - "@id": "bts:GenomicsAssay" + "@id": "bts:BodyPart" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "readDepth", + "sms:displayName": "scalp", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Bulk", + "@id": "bts:Pelvis", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Bulk", + "rdfs:label": "Pelvis", "rdfs:subClassOf": [ { - "@id": "bts:DissociationMethod" + "@id": "bts:BodyPart" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "bulk", + "sms:displayName": "pelvis", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:None", + "@id": "bts:Neck", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "None", + "rdfs:label": "Neck", "rdfs:subClassOf": [ { - "@id": "bts:DissociationMethod" + "@id": "bts:BodyPart" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "none", + "sms:displayName": "neck", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TransplantationRecipientTissue", + "@id": "bts:Leg", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "TransplantationRecipientTissue", + "rdfs:label": "Leg", "rdfs:subClassOf": [ { - "@id": "bts:Xenograft" + "@id": "bts:BodyPart" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "transplantationRecipientTissue", + "sms:displayName": "leg", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Liver", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Liver", + "rdfs:subClassOf": [ + { + "@id": "bts:Organ" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "liver", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Axilla", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Axilla", + "rdfs:subClassOf": [ + { + "@id": "bts:BodyPart" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "axilla", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Acetabulum", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Acetabulum", + "rdfs:subClassOf": [ + { + "@id": "bts:BodyPart" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "acetabulum", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Forearm", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Forearm", + "rdfs:subClassOf": [ + { + "@id": "bts:BodyPart" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "forearm", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Muscle", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Muscle", + "rdfs:subClassOf": [ + { + "@id": "bts:BodyPart" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "muscle", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Finger", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Finger", + "rdfs:subClassOf": [ + { + "@id": "bts:BodyPart" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "finger", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Thoracicspine", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Thoracicspine", + "rdfs:subClassOf": [ + { + "@id": "bts:BodyPart" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "thoracic spine", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Groin", + "@type": "rdfs:Class", + "rdfs:comment": "Anatomically also known as the inguinal part of abdomen.", + "rdfs:label": "Groin", + "rdfs:subClassOf": [ + { + "@id": "bts:BodyPart" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "groin", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Back", + "@type": "rdfs:Class", + "rdfs:comment": "Anatomically also known as the dorsum.", + "rdfs:label": "Back", + "rdfs:subClassOf": [ + { + "@id": "bts:BodyPart" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "back", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Iliacspine", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Iliacspine", + "rdfs:subClassOf": [ + { + "@id": "bts:BodyPart" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "iliac spine", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Spine", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Spine", + "rdfs:subClassOf": [ + { + "@id": "bts:BodyPart" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "spine", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Shoulder", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Shoulder", + "rdfs:subClassOf": [ + { + "@id": "bts:BodyPart" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "shoulder", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Scapula", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Scapula", + "rdfs:subClassOf": [ + { + "@id": "bts:BodyPart" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "scapula", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CuratedData", + "@type": "rdfs:Class", + "rdfs:comment": "Any file derived from or pertaining a manually or programatically curated data resource. Examples include: reference sequences, drug information databases, identifier maps\"", + "rdfs:label": "CuratedData", + "rdfs:subClassOf": [ + { + "@id": "schema:Thing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "curatedData", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TransplantationRecipientTissue", + "@type": "rdfs:Class", + "rdfs:comment": "Tissue into which a xenograph sample is transplanted", + "rdfs:label": "TransplantationRecipientTissue", + "rdfs:subClassOf": [ + { + "@id": "schema:Thing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "transplantationRecipientTissue", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Tumor-adjacentnormal", + "@type": "rdfs:Class", + "rdfs:comment": "Tissue comprised of morphologically normal tissue collected from the area immediately surrounding a tumor.", + "rdfs:label": "Tumor-adjacentnormal", + "rdfs:subClassOf": [ + { + "@id": "bts:Tissue" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "tumor-adjacent normal", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PDXtissue", + "@type": "rdfs:Class", + "rdfs:comment": "Patient derived xenograft tissue", + "rdfs:label": "PDXtissue", + "rdfs:subClassOf": [ + { + "@id": "bts:Tissue" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "PDX tissue", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CDXtissue", + "@type": "rdfs:Class", + "rdfs:comment": "Cell line derived xenograft tissue", + "rdfs:label": "CDXtissue", + "rdfs:subClassOf": [ + { + "@id": "bts:Tissue" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "CDX tissue", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Tumor", + "@type": "rdfs:Class", + "rdfs:comment": "General term for tumor sample – use when it is unknown when a more specific clinical classification is unknown, e.g. whether it is primary or secondary.", + "rdfs:label": "Tumor", + "rdfs:subClassOf": [ + { + "@id": "bts:Tissue" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "tumor", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Metastatictumor", + "@type": "rdfs:Class", + "rdfs:comment": "For neoplasms, a non-infiltrating and non-metastasizing neoplastic process that is characterized by the absence of morphologic features associated with malignancy (e.g., severe atypia, nuclear pleomorphism, tumor cell necrosis, and abnormal mitoses).", + "rdfs:label": "Metastatictumor", + "rdfs:subClassOf": [ + { + "@id": "bts:Tissue" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "metastatic tumor", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Metastatic/recurrenttumor", + "@type": "rdfs:Class", + "rdfs:comment": "A tumor with metastatic/recurrent characteristic.", + "rdfs:label": "Metastatic/recurrenttumor", + "rdfs:subClassOf": [ + { + "@id": "bts:Tissue" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "metastatic/recurrent tumor", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Recurrenttumor", + "@type": "rdfs:Class", + "rdfs:comment": "A tumor described with recurrent characteristic.", + "rdfs:label": "Recurrenttumor", + "rdfs:subClassOf": [ + { + "@id": "bts:Tissue" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "recurrent tumor", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TRUE", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "TRUE", + "rdfs:subClassOf": [ + { + "@id": "bts:IsCellLine" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "TRUE", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:FALSE", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "FALSE", + "rdfs:subClassOf": [ + { + "@id": "bts:IsCellLine" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "FALSE", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Nuclei", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Nuclei", + "rdfs:subClassOf": [ + { + "@id": "bts:ProteinExtractSource" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "nuclei", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ChIPseq", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "ChIPseq", + "rdfs:subClassOf": [ + { + "@id": "bts:ImmunoAssayType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "ChIPseq", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ATAC-seq", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "ATAC-seq", + "rdfs:subClassOf": [ + { + "@id": "bts:ImmunoAssayType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "ATAC-seq", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:+/?", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "+/?", + "rdfs:subClassOf": [ + { + "@id": "bts:Nf2Genotype" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "+/?", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:-/?", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "-/?", + "rdfs:subClassOf": [ + { + "@id": "bts:Nf2Genotype" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "-/?", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ModelSystemStrainNomenclature", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "ModelSystemStrainNomenclature", + "rdfs:subClassOf": [ + { + "@id": "bts:GenomicsAssay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "modelSystemStrainNomenclature", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ReadDepth", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "ReadDepth", + "rdfs:subClassOf": [ + { + "@id": "bts:GenomicsAssay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "readDepth", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Bulk", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Bulk", + "rdfs:subClassOf": [ + { + "@id": "bts:DissociationMethod" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "bulk", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:None", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "None", + "rdfs:subClassOf": [ + { + "@id": "bts:DissociationMethod" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "none", "sms:required": "sms:false", "sms:validationRules": [] },