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Merge pull request #1265 from EBISPOT/3.34.0
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EFO release 3.34.0
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zoependlington authored Sep 15, 2021
2 parents dc9c576 + b21eda4 commit 3f36c63
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7,411 changes: 1,078 additions & 6,333 deletions ExFactor Ontology release notes.txt

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17 changes: 13 additions & 4 deletions efo-base.owl
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xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
xmlns:patterns="http://www.co-ode.org/patterns#">
<owl:Ontology rdf:about="http://www.ebi.ac.uk/efo/efo-base.owl">
<owl:versionIRI rdf:resource="http://www.ebi.ac.uk/efo/releases/v3.33.0/efo-base.owl"/>
<owl:versionIRI rdf:resource="http://www.ebi.ac.uk/efo/releases/v3.34.0/efo-base.owl"/>
<obo:format-version rdf:datatype="http://www.w3.org/2001/XMLSchema#string">1.4</obo:format-version>
<dc:creator>Gautier Koscielny</dc:creator>
<dc:creator>Laura Huerta Martinez</dc:creator>
Expand All @@ -40,8 +40,8 @@ License. </dc:rights>
<efo:creator>Simon Jupp</efo:creator>
<efo:creator>Sirarat Sarntivijai</efo:creator>
<efo:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Tomasz Adamusiak</efo:creator>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2021-09-14</rdfs:comment>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">3.33.0</owl:versionInfo>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2021-09-15</rdfs:comment>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">3.34.0</owl:versionInfo>
</owl:Ontology>


Expand Down Expand Up @@ -422341,6 +422341,7 @@ The procedure involves either a single lung transplant, bilateral sequential lun
<dc:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#string">paola</dc:creator>
<oboInOwl:hasNarrowSynonym>breast milk expression</oboInOwl:hasNarrowSynonym>
<oboInOwl:hasNarrowSynonym>breast milk pumping</oboInOwl:hasNarrowSynonym>
<oboInOwl:inSubset rdf:resource="http://www.ebi.ac.uk/efo/added_for_HCA"/>
<rdfs:label>breast milk collection</rdfs:label>
</owl:Class>
<owl:Axiom>
Expand All @@ -422360,6 +422361,7 @@ The procedure involves either a single lung transplant, bilateral sequential lun
<obo:IAO_0000115>Next generation one-cell sequencing (Nx1-seq) is a single cell transcriptomic library preparation method which conjugates polystyrene beads to barcode nucleotides by means of emulsion PCR using oligo-dTs. The beads are mixed on a chamber slide containing PDMS microwells which fit one cell per well. The slide is then washed with a cell suspension to capture and barcode individual cells.</obo:IAO_0000115>
<dc:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#string">paola</dc:creator>
<oboInOwl:hasExactSynonym>next generation one-cell sequencing</oboInOwl:hasExactSynonym>
<oboInOwl:inSubset rdf:resource="http://www.ebi.ac.uk/efo/added_for_HCA"/>
<rdfs:label>Nx1-seq</rdfs:label>
</owl:Class>
<owl:Axiom>
Expand All @@ -422378,6 +422380,7 @@ The procedure involves either a single lung transplant, bilateral sequential lun
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<obo:IAO_0000115>A data transformation process involved in generating a raw matrix from raw data.</obo:IAO_0000115>
<dc:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#string">paola</dc:creator>
<oboInOwl:inSubset rdf:resource="http://www.ebi.ac.uk/efo/added_for_HCA"/>
<rdfs:label>raw matrix generation</rdfs:label>
</owl:Class>
<owl:Axiom>
Expand All @@ -422396,6 +422399,7 @@ The procedure involves either a single lung transplant, bilateral sequential lun
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<obo:IAO_0000115>A data transformation process involved in generating a processed matrix from sequence data and/or count matrices, including demultiplexing samples, quality control, normalization, data correction, and feature selection.</obo:IAO_0000115>
<dc:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#string">paola</dc:creator>
<oboInOwl:inSubset rdf:resource="http://www.ebi.ac.uk/efo/added_for_HCA"/>
<rdfs:label>processed matrix generation</rdfs:label>
</owl:Class>
<owl:Axiom>
Expand All @@ -422413,6 +422417,7 @@ The procedure involves either a single lung transplant, bilateral sequential lun
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<obo:IAO_0000115>A data transformation process involved in analysing expression matrices, including visualisation, comparison or integration with other datasets, clustering, and differential expression analysis.</obo:IAO_0000115>
<dc:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#string">paola</dc:creator>
<oboInOwl:inSubset rdf:resource="http://www.ebi.ac.uk/efo/added_for_HCA"/>
<rdfs:label>analysis of matrices</rdfs:label>
</owl:Class>
<owl:Axiom>
Expand All @@ -422431,6 +422436,7 @@ The procedure involves either a single lung transplant, bilateral sequential lun
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0200000"/>
<obo:IAO_0000115>A data transformation process involved in analysing spatial images or data.</obo:IAO_0000115>
<dc:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#string">paola</dc:creator>
<oboInOwl:inSubset rdf:resource="http://www.ebi.ac.uk/efo/added_for_HCA"/>
<rdfs:label>spatial analysis</rdfs:label>
</owl:Class>
<owl:Axiom>
Expand Down Expand Up @@ -422487,6 +422493,7 @@ The procedure involves either a single lung transplant, bilateral sequential lun
<dc:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#string">paola</dc:creator>
<oboInOwl:hasExactSynonym>Sci-RNA-Seq3</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym>sci-RNA-Seq3</oboInOwl:hasExactSynonym>
<oboInOwl:inSubset rdf:resource="http://www.ebi.ac.uk/efo/added_for_HCA"/>
<rdfs:label>sci-RNA-seq3</rdfs:label>
</owl:Class>
<owl:Axiom>
Expand All @@ -422506,6 +422513,7 @@ The procedure involves either a single lung transplant, bilateral sequential lun
<dc:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#string">paola</dc:creator>
<oboInOwl:hasBroadSynonym>digital spatial profiling</oboInOwl:hasBroadSynonym>
<oboInOwl:hasExactSynonym>nanoString digital spatial profiling (DSP)</oboInOwl:hasExactSynonym>
<oboInOwl:inSubset rdf:resource="http://www.ebi.ac.uk/efo/added_for_HCA"/>
<rdfs:label>nanoString digital spatial profiling</rdfs:label>
</owl:Class>
<owl:Axiom>
Expand Down Expand Up @@ -422545,6 +422553,7 @@ The procedure involves either a single lung transplant, bilateral sequential lun
<obo:IAO_0000115>The SCOPE-chip captures single cells by partitioning them into hundreds of thousands of microwells on the chip following the Poisson distribution. Afterwards, an excess of Barcoding Beads is added to the microwells of the chip; the diameter of the beads versus that of the microwells ensuring that only one Barcoding Bead falls into each microwell. After cell lysis, Barcoding Beads, each with a unique cell label (Barcode), capture mRNA by binding to the poly (A) tail. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads into cDNA, and subsequent PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters. The end result is an NGS library that is compatible with Illumina sequencing instruments, that can also be run on Pacbio and MGI sequencing platforms with minor modifications.</obo:IAO_0000115>
<dc:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#string">paola</dc:creator>
<oboInOwl:hasExactSynonym>GEXSCOPE</oboInOwl:hasExactSynonym>
<oboInOwl:inSubset rdf:resource="http://www.ebi.ac.uk/efo/added_for_HCA"/>
<rdfs:label>SCOPE-chip</rdfs:label>
</owl:Class>
<owl:Axiom>
Expand Down Expand Up @@ -492550,7 +492559,7 @@ Use: http://www.ebi.ac.uk/efo/EFO_0000197 Label: mucinous carcinoma</efo:reason_
<owl:annotatedSource rdf:resource="http://www.ebi.ac.uk/efo/EFO_1000576"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
<owl:annotatedTarget>carcinoma of thymus</owl:annotatedTarget>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MONDO:patterns/carcinoma</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref>MONDO:patterns/carcinoma</oboInOwl:hasDbXref>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://www.ebi.ac.uk/efo/EFO_1000576"/>
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