Add explicit preferred prefixes for a subset of ontologies

For now, this skips obsolete ontologies, inactive ontologies, and orphaned ontologies.

ontology/aeo.md

@@ -21,6 +21,7 @@ build:
   method: vcs
 activity_status: active
 repository: https://github.com/obophenotype/human-developmental-anatomy-ontology
+preferredPrefix: AEO
 ---
 
 The AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology, to about 160 classes using the is_a relationship; it thus provides a detailed type classification for tissues. The ~100 new classes were chosen for their use in categorizing the major vertebrate and invertebrate anatomy ontologies at a granularity adequate for tissues of a single cell type. This site is to be used for posting details of the ontologies and updates

ontology/agro.md

@@ -37,6 +37,7 @@ build:
 tracker: https://github.com/AgriculturalSemantics/agro/issues/
 activity_status: active
 repository: https://github.com/AgriculturalSemantics/agro
+preferredPrefix: AGRO
 ---
 
 AgrO, the Agronomy Ontology, describes agronomic practices, techniques, and variables used in agronomic experiments. AgrO is being built using traits identified by agronomists, the ICASA variables, and other existing ontologies such as ENVO, UO, PATO, IAO, and CHEBI. Further, AgrO powers AgroFIMS, the Agronomy Fieldbook and Information Management System modeled on a CGIAR Breeding Management System to capture agronomic data.

ontology/aism.md

@@ -29,6 +29,7 @@ license:
   label: CC-BY
 activity_status: active
 repository: https://github.com/insect-morphology/aism
+preferredPrefix: AISM
 ---
 
 The AISM contains terms used in insect biodiversity research for describing structures of the exoskeleton and the skeletomuscular system. It aims to serve as the basic backbone of generalized terms to be expanded with order-specific terminology.

ontology/amphx.md

@@ -23,6 +23,7 @@ license:
   label: CC-BY
 activity_status: active
 repository: https://github.com/EBISPOT/amphx_ontology
+preferredPrefix: AMPHX
 ---
 
 The Amphioxus Development and Anatomy Ontology (AMPHX) is to describe the anatomy and development of Amphioxus, also known as lancelet, member of the invertebrate subphylum Cephalochordata and the phylum Chordata. This ontology is intended to be used for description of gene expression in amphioxus (e.g. Insitus, RNA-seq). The ontology was created in the context of the European project CORBEL (https://www.corbel-project.eu/home.html), and used in the database MARIMBA (http://marimba.obs-vlfr.fr/home).

ontology/apo.md

@@ -24,6 +24,7 @@ build:
   method: obo2owl
 activity_status: active
 repository: https://github.com/obophenotype/ascomycete-phenotype-ontology
+preferredPrefix: APO
 ---
 
 A structured controlled vocabulary for the phenotypes of Ascomycete fungi

ontology/apollo_sv.md

@@ -16,6 +16,7 @@ license:
   url: https://creativecommons.org/licenses/by/3.0/
   label: CC-BY 3.0
 repository: https://github.com/ApolloDev/apollo-sv
+preferredPrefix: APOLLO_SV
 ---
 
 #Apollo Structured Vocabulary

ontology/aro.md

@@ -17,6 +17,7 @@ products:
   - id: aro.owl
 activity_status: active
 repository: https://github.com/arpcard/aro
+preferredPrefix: ARO
 ---
 
 The Antibiotic Resistance Ontology

ontology/bco.md

@@ -18,6 +18,7 @@ title: Biological Collections Ontology
 tracker: https://github.com/tucotuco/bco/issues
 activity_status: active
 repository: https://github.com/tucotuco/bco
+preferredPrefix: BCO
 ---
 
 The Biological Collections Ontology (BCO) is a being developed as an application ontology as part of the Biocode Commons project, within the OBO Foundry framework. The goal of the BCO is to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys.

ontology/bfo.md

@@ -35,6 +35,7 @@ usages:
     description: BFO is imported by multiple OBO ontologies to standardize upper level structure
 activity_status: active
 repository: https://github.com/BFO-ontology/BFO
+preferredPrefix: BFO
 ---
 
 BFO grows out of a philosophical orientation which overlaps with that of DOLCE and SUMO. Unlike these, however, it is narrowly focused on the task of providing a genuine upper ontology which can be used in support of domain ontologies developed for scientific research, as for example in biomedicine within the framework of the OBO Foundry. Thus BFO does not contain physical, chemical, biological or other terms which would properly fall within the special sciences domains. BFO is the upper level ontology upon which OBO Foundry ontologies are built.

ontology/bspo.md

@@ -27,6 +27,7 @@ publications:
     title: "Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology."
 activity_status: active
 repository: https://github.com/obophenotype/biological-spatial-ontology
+preferredPrefix: BSPO
 ---
 
 An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies.

ontology/bto.md

@@ -26,6 +26,7 @@ build:
   path: "."
 activity_status: active
 repository: https://github.com/BRENDA-Enzymes/BTO
+preferredPrefix: BTO
 ---
 
 A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.

ontology/caro.md

@@ -21,6 +21,7 @@ build:
 tracker: https://github.com/obophenotype/caro/issues
 activity_status: active
 repository: https://github.com/obophenotype/caro
+preferredPrefix: CARO
 ---
 
 The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO will be described in Anatomy Ontologies for Bioinformatics: Principles and Practice Albert Burger, Duncan Davidson and Richard Baldock (Editors)

ontology/cdao.md

@@ -18,6 +18,7 @@ license:
   label: CC0 1.0 Universal
 activity_status: active
 repository: https://github.com/evoinfo/cdao
+preferredPrefix: CDAO
 ---
 
 A formalization of concepts and relations relevant to evolutionary comparative analysis, such as phylogenetic trees, OTUs (operational taxonomic units) and compared characters (including molecular characters as well as other types). CDAO is being developed by scientists in biology, evolution, and computer science

ontology/cdno.md

@@ -30,6 +30,7 @@ license:
   label: CC-BY
 activity_status: active
 repository: https://github.com/Southern-Cross-Plant-Science/cdno
+preferredPrefix: CDNO
 ---
 
 The CDNO provides structured terminologies to describe nutritional attributes of material entities that contribute to human diet. These terms are intended primarily to be associated with datasets that quantify concentration of chemical nutritional components derived from samples taken from any stage in the production of food raw materials (including from crops, livestock, fisheries) and through processing and supply chains. Additional knowledge associated with these dietary sources may be represented by terms that describe functional, physical and other attributes. 

ontology/chebi.md

@@ -53,6 +53,7 @@ usages:
         description: "A curated zebrafish experiment involving exposure to (5Z,8Z,14Z)-11,12-dihydroxyicosatrienoic acid (CHEBI:63969)"
 activity_status: active
 repository: https://github.com/ebi-chebi/ChEBI
+preferredPrefix: CHEBI
 ---
 
 A freely available dictionary of molecular entities focused on ‘small’ chemical compounds.

ontology/cheminf.md

@@ -20,6 +20,7 @@ build:
   method: owl2obo
 activity_status: active
 repository: https://github.com/semanticchemistry/semanticchemistry
+preferredPrefix: CHEMINF
 ---
 
 Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them.

ontology/chiro.md

@@ -36,4 +36,5 @@ license:
   label: CC-0
 activity_status: active
 repository: https://github.com/obophenotype/chiro
+preferredPrefix: CHIRO
 ---

ontology/chmo.md

@@ -18,6 +18,7 @@ title: Chemical Methods Ontology
 tracker: https://github.com/rsc-ontologies/rsc-cmo/issues
 activity_status: active
 repository: https://github.com/rsc-ontologies/rsc-cmo
+preferredPrefix: CHMO
 ---
 
 CHMO, the chemical methods ontology, describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy prepare and separate material for further analysis, such as sample ionisation, chromatography, and electrophoresis synthesise materials, such as epitaxy and continuous vapour deposition It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI).

ontology/cido.md

@@ -16,6 +16,7 @@ license:
   label: CC-BY
 activity_status: active
 repository: https://github.com/cido-ontology/cido
+preferredPrefix: CIDO
 ---
 
 The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, epidemiology, pathogenesis, diagnosis, prevention, and treatment. Its development follows the OBO Foundry Principles.

ontology/cio.md

@@ -17,6 +17,7 @@ products:
   - id: cio.obo
 activity_status: active
 repository: https://github.com/BgeeDB/confidence-information-ontology
+preferredPrefix: CIO
 ---
 
 The Confidence Information Ontology (CIO) is an ontology to capture confidence information about annotations.

ontology/cl.md

@@ -73,6 +73,7 @@ usages:
         description: FANTOM5 samples annotated to neuron
 activity_status: active
 repository: https://github.com/obophenotype/cell-ontology
+preferredPrefix: CL
 ---
 
 ![logo](/images/CL-logo.jpg)

ontology/clao.md

@@ -24,6 +24,7 @@ license:
   label: CC-0
 activity_status: active
 repository: https://github.com/luis-gonzalez-m/Collembola
+preferredPrefix: CLAO
 ---
 
 CLAO includes 1201 classes related mainly with anatomical systems, sclerites, and chaetotaxy. This ontology should increase the anatomical knowledge in Arthropoda and interoperability with other anatomical ontologies as HAO.

ontology/clo.md

@@ -20,6 +20,7 @@ license:
   label: CC-BY
 activity_status: active
 repository: https://github.com/CLO-Ontology/CLO
+preferredPrefix: CLO
 ---
 
 # Summary

ontology/clyh.md

@@ -26,6 +26,7 @@ license:
   label: CC-BY
 activity_status: active
 repository: https://github.com/EBISPOT/clyh_ontology
+preferredPrefix: CLYH
 ---
 
 The Clytia hemisphaerica Development and Anatomy Ontology (CLYH) describes the anatomical and developmental features of the Clytia hemisphaerica life cycle. This species is a member of the phylum Cnidaria and belongs to the hydrozoan clade Leptothecata. Its life cycle comprises three stages: a planula larva, a benthic polyp colony, and a sexually-reproducing jellyfish  (medusa).

ontology/cmo.md

@@ -30,6 +30,7 @@ browsers:
     url: http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=CMO:0000000
 activity_status: active
 repository: https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology
+preferredPrefix: CMO
 ---
 
 <img src="http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif"/>

ontology/cob.md

@@ -17,6 +17,7 @@ license:
 title: Core Ontology for Biology and Biomedicine
 activity_status: active
 repository: https://github.com/OBOFoundry/COB
+preferredPrefix: COB
 ---
 
 The Core Ontology for Biology and Biomedicine (COB) brings together key terms from a wide range of OBO projects into a single, small ontology. The goal is to improve interoperabilty and reuse across the OBO community through better coordination of key terms.

ontology/cro.md

@@ -22,6 +22,7 @@ products:
     title: CRO
 activity_status: active
 repository: https://github.com/data2health/contributor-role-ontology
+preferredPrefix: CRO
 ---
 
 The Contributor Role Ontology expands the CASRAI Contributor Roles Taxonomy (CRediT), which is a high-level classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability.

ontology/cteno.md

@@ -31,6 +31,7 @@ license:
   label: CC-BY
 activity_status: active
 repository: https://github.com/obophenotype/ctenophore-ontology
+preferredPrefix: CTENO
 ---
 
 An anatomical and developmental ontology for ctenophores (Comb Jellies).

ontology/cto.md

@@ -16,6 +16,7 @@ license:
   label: CC-BY
 activity_status: active
 repository: https://github.com/ClinicalTrialOntology/CTO
+preferredPrefix: CTO
 ---
 
 The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials.

ontology/cvdo.md

@@ -19,6 +19,7 @@ build:
 tracker: https://github.com/OpenLHS/CVDO/issues
 activity_status: active
 repository: https://github.com/OpenLHS/CVDO
+preferredPrefix: CVDO
 ---
 
 CVDO is an ontology based on the OGMS model of disease, designed to describe entities related to cardiovascular diseases (including the diseases themselves, the underlying disorders, and the related pathological processes). It is being developed at Sherbrooke University (Canada) and the INSERM research institute (Institut National de la Santé et de la Recherche Médicale).

ontology/ddanat.md

@@ -26,6 +26,7 @@ build:
 tracker: https://github.com/dictyBase/migration-data/issues
 activity_status: active
 repository: https://github.com/dictyBase/migration-data
+preferredPrefix: DDANAT
 ---
 
 A structured controlled vocabulary of the anatomy of the slime-mould <i>Dictyostelium discoideum</i>.

ontology/ddpheno.md

@@ -26,4 +26,5 @@ build:
   path: "."
 activity_status: active
 repository: https://github.com/obophenotype/dicty-phenotype-ontology
+preferredPrefix: DDPHENO
 ---

ontology/dideo.md

@@ -16,6 +16,7 @@ products:
   - id: dideo.owl
 activity_status: active
 repository: https://github.com/DIDEO/DIDEO
+preferredPrefix: DIDEO
 ---
 
 DIDEO is created as part of an NIH-funded project aiming towards developing a new knowledge base for potential drug drug interaction information. In DIDEO we represent PDDIs as information content entities and we aim to also provide the evidence for those entities using nano- and micro publication approaches.

ontology/doid.md

@@ -62,6 +62,7 @@ usages:
         description: Search for experimental data on antibody and T cell epitopes associated with human diseases in the DO. To search for DO disease terms, use the Disease search box on the front page.
 activity_status: active
 repository: https://github.com/DiseaseOntology/HumanDiseaseOntology
+preferredPrefix: DOID
 ---
 
 Creating a comprehensive classification of human diseases organized by etiology.

ontology/dron.md

@@ -19,6 +19,7 @@ license:
   label: CC-BY
 activity_status: active
 repository: https://github.com/ufbmi/dron/
+preferredPrefix: DRON
 ---
 
 We built this ontology primarily to support comparative effectiveness researchers studying claims data. They need to be able to query U.S. National Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade), physiological effect (diuresis), and therapeutic intent (anti-hypertensive).

ontology/duo.md

@@ -26,6 +26,7 @@ license:
   label: CC-BY
 activity_status: active
 repository: https://github.com/EBISPOT/DUO
+preferredPrefix: DUO
 ---
 
 DUO allows to semantically tag datasets with restriction about their usage, making them discoverable automatically based on the authorization level of users, or intended usage.

ontology/ecao.md

@@ -26,6 +26,7 @@ license:
   label: CC-BY
 activity_status: active
 repository: https://github.com/echinoderm-ontology/ecao_ontology
+preferredPrefix: ECAO
 ---
 
 This ontology is intended to be used for the description and curation of information related to gene regulatory processes in echinoderms (e.g., expression patterns of endogenous genes and reporter DNA constructs, phenotypic effects of gene perturbations, etc.). 

ontology/eco.md

@@ -49,6 +49,7 @@ usages:
         title: "The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species"
 activity_status: active
 repository: https://github.com/evidenceontology/evidenceontology
+preferredPrefix: ECO
 ---
 
 <img src="https://avatars1.githubusercontent.com/u/12802432" alt="ECO logo"/>

ontology/ecocore.md

@@ -36,6 +36,7 @@ license:
   label: CC-BY
 activity_status: active
 repository: https://github.com/EcologicalSemantics/ecocore
+preferredPrefix: ECOCORE
 ---
 
 This ontology aims to provide core semantics for ecological entities, such as ecological functions (for predators, prey, etc), food webs, and ecological interactions. The ontology, closely interoperates with existing OBO ontologies such as the Environment Ontology, the Population and Community Ontology (PCO), the Relations Ontology (RO), the Gene Ontology (for biological processes etc), the Phenotype and Quality Ontology (PATO), the Plant Ontology (PO), and many others. Ecocore is under active development.

ontology/ecto.md

@@ -51,5 +51,6 @@ license:
   label: CC0
 activity_status: active
 repository: https://github.com/EnvironmentOntology/environmental-exposure-ontology
+preferredPrefix: ECTO
 ---
 <img src="https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/ecto-logos/ecto-logo_black-banner.png"/>

ontology/emapa.md

@@ -29,6 +29,7 @@ usages:
     description: GXD
 activity_status: active
 repository: https://github.com/obophenotype/mouse-anatomy-ontology
+preferredPrefix: EMAPA
 ---
 
 ## BACKGROUND

ontology/envo.md

@@ -83,6 +83,7 @@ build:
 tracker: https://github.com/EnvironmentOntology/envo/issues/
 activity_status: active
 repository: https://github.com/EnvironmentOntology/envo
+preferredPrefix: ENVO
 ---
 
 EnvO is a community ontology for the concise, controlled description of environments.

ontology/eupath.md

@@ -29,6 +29,7 @@ usages:
 
 activity_status: active
 repository: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology
+preferredPrefix: EUPATH
 ---
 
 The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host & Vector Genomics Resource (VEuPathDB; https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available.

ontology/fao.md

@@ -26,6 +26,7 @@ build:
   infallible: 1
 activity_status: active
 repository: https://github.com/obophenotype/fungal-anatomy-ontology
+preferredPrefix: FAO
 ---
 
 ![FAO image](http://www.yeastgenome.org/images/fao.color.png)

ontology/fideo.md

@@ -17,6 +17,7 @@ license:
 tracker: https://github.com/getbordea/fideo/issues
 activity_status: active
 repository: https://github.com/getbordea/fideo
+preferredPrefix: FIDEO
 ---
 
 FIDEO represents food-drug interactions automatically extracted from scientific literature.

ontology/flopo.md

@@ -23,4 +23,5 @@ title: Flora Phenotype Ontology
 tracker: https://github.com/flora-phenotype-ontology/flopoontology/issues
 activity_status: active
 repository: https://github.com/flora-phenotype-ontology/flopoontology
+preferredPrefix: FLOPO
 ---

ontology/fma.md

@@ -30,6 +30,7 @@ build:
   method: obo2owl
 tracker: https://sourceforge.net/p/obo/foundational-model-of-anatomy-fma-requests/
 activity_status: active
+preferredPrefix: FMA
 ---
 
 Obo format translation of the FMA, omitting all relationships other than is_a, part_of and has_part. Future versions of fma_obo will include more relationships