Harmonising domains for all ontologies (OBOFoundry#1810)

* Harmonising domains for all ontologies

* Revert "Harmonising domains for all ontologies"

This reverts commit c2a945c.

* Changing to have two spaces

* Update registry_schema.json

* Update registry_schema.json

* Update registry_schema.json

* Update registry_schema.json

* Update ontology/ontoneo.md

Co-authored-by: Charles Tapley Hoyt <[email protected]>

* Update ontology/oae.md

Co-authored-by: Charles Tapley Hoyt <[email protected]>

* Update ontology/ecocore.md

Co-authored-by: Charles Tapley Hoyt <[email protected]>

* Update ontology/eupath.md

Co-authored-by: Charles Tapley Hoyt <[email protected]>

* Update ontology/opl.md

Co-authored-by: Charles Tapley Hoyt <[email protected]>

* Update ontology/sepio.md

Co-authored-by: Charles Tapley Hoyt <[email protected]>

* Update ontology/obib.md

Co-authored-by: Charles Tapley Hoyt <[email protected]>

* Update ecocore.md

* Update ontology/rbo.md

Co-authored-by: Charles Tapley Hoyt <[email protected]>

* Update ontology/one.md

Co-authored-by: Charles Tapley Hoyt <[email protected]>

* Update ontology/lepao.md

Co-authored-by: Charles Tapley Hoyt <[email protected]>

* Update ontology/colao.md

Co-authored-by: Charles Tapley Hoyt <[email protected]>

* Update ontology/fobi.md

Co-authored-by: Charles Tapley Hoyt <[email protected]>

* Update ontology/one.md

Co-authored-by: Charles Tapley Hoyt <[email protected]>

* Update ontology/foodon.md

Co-authored-by: Charles Tapley Hoyt <[email protected]>

* Update ontology/ons.md

Co-authored-by: Charles Tapley Hoyt <[email protected]>

* Update util/schema/registry_schema.json

Co-authored-by: Charles Tapley Hoyt <[email protected]>

* Remove other, add "simulation"

* Update pso.md

* Fixing two metadata elements

* Changes experiments to investigations

see OBOFoundry#1225 (comment)

Co-authored-by: Charles Tapley Hoyt <[email protected]>

ontology/aeo.md

@@ -8,7 +8,7 @@ license:
   url: https://creativecommons.org/licenses/by/4.0/
   label: CC BY 4.0
 description: AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology
-domain: anatomy
+domain: anatomy and development
 homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology/
 tracker: https://github.com/obophenotype/human-developmental-anatomy-ontology/issues
 products:

ontology/agro.md

@@ -5,7 +5,9 @@ title: Agronomy Ontology
 license:
   url: https://creativecommons.org/licenses/by/4.0/
   label: CC BY 4.0
-domain: agronomy
+domain: agriculture
+tags:
+  - agronomy
 build:
   checkout: git clone  https://github.com/AgriculturalSemantics/agro.git
   system: git

ontology/aism.md

@@ -12,7 +12,7 @@ contact:
   github: JCGiron
   orcid: 0000-0002-0851-6883
 description: 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.
-domain: anatomy
+domain: anatomy and development
 homepage: https://github.com/insect-morphology/aism
 products:
   - id: aism.owl

ontology/amphx.md

@@ -12,7 +12,7 @@ contact:
   github: hescriva
   orcid: 0000-0001-7577-5028
 description: An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum).
-domain: anatomy
+domain: anatomy and development
 homepage: https://github.com/EBISPOT/amphx_ontology
 products:
   - id: amphx.owl

ontology/bco.md

@@ -11,7 +11,9 @@ license:
   url: https://creativecommons.org/publicdomain/zero/1.0/
   label: CC0 1.0
 description: An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys.
-domain: biodiversity collections
+domain: organisms
+tags:
+  - biodiversity collections
 homepage: https://github.com/BiodiversityOntologies/bco
 products:
   - id: bco.owl

ontology/bila.md

@@ -4,7 +4,7 @@ id: bila
 contact:
   email: [email protected]
   label: Thorsten Heinrich
-domain: anatomy
+domain: anatomy and development
 homepage: http://4dx.embl.de/4DXpress
 products:
   - id: bila.owl

ontology/bspo.md

@@ -7,7 +7,7 @@ contact:
   github: cmungall
   orcid: 0000-0002-6601-2165
 description: An ontology for representing spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces
-domain: anatomy
+domain: anatomy and development
 homepage: https://github.com/obophenotype/biological-spatial-ontology
 products:
   - id: bspo.owl

ontology/bto.md

@@ -7,7 +7,7 @@ contact:
   github: chdudek
   orcid: 0000-0001-9117-7909
 description: A structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures.
-domain: anatomy
+domain: anatomy and development
 homepage: http://www.brenda-enzymes.org
 tracker: https://github.com/BRENDA-Enzymes/BTO/issues
 page: https://en.wikipedia.org/wiki/BRENDA_tissue_ontology

ontology/caro.md

@@ -10,7 +10,7 @@ license:
   url: https://creativecommons.org/licenses/by/3.0/
   label: CC BY 3.0
 description: An upper level ontology to facilitate interoperability between existing anatomy ontologies for different species
-domain: anatomy
+domain: anatomy and development
 homepage: https://github.com/obophenotype/caro/
 products:
   - id: caro.owl

ontology/cdno.md

@@ -12,7 +12,7 @@ contact:
   github: LilyAndres
   orcid: 0000-0002-7696-731X
 description: CDNO provides structured terminologies to describe nutritional attributes of material entities that contribute to human diet.
-domain: diet, metabolomics and nutrition
+domain: diet, metabolomics, and nutrition
 homepage: https://github.com/Southern-Cross-Plant-Science/cdno
 products:
   - id: cdno.owl

ontology/ceph.md

@@ -13,7 +13,7 @@ contact:
   github: cmungall
   orcid: 0000-0002-6601-2165
 description: An anatomical and developmental ontology for cephalopods
-domain: anatomy
+domain: anatomy and development
 homepage: https://github.com/obophenotype/cephalopod-ontology
 products:
   - id: ceph.owl

ontology/cl.md

@@ -26,7 +26,9 @@ license:
 taxon:
   id: NCBITaxon:33208
   label: Metazoa
-domain: cells
+domain: anatomy and development
+tags:
+  - cells
 tracker: https://github.com/obophenotype/cell-ontology/issues
 mailing_list: https://groups.google.com/g/cl_edit
 publications:

ontology/clao.md

@@ -12,7 +12,7 @@ contact:
   github: luis-gonzalez-m
   orcid: 0000-0002-9136-9932
 description: "CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda)."
-domain: anatomy
+domain: anatomy and development
 homepage: https://github.com/luis-gonzalez-m/Collembola
 products:
   - id: clao.owl

ontology/clyh.md

@@ -12,7 +12,7 @@ contact:
   github: L-Leclere
   orcid: 0000-0002-7440-0467
 description: The Clytia hemisphaerica Development and Anatomy Ontology (CLYH) describes the anatomical and developmental features of the Clytia hemisphaerica life cycle.
-domain: anatomy
+domain: anatomy and development
 homepage: https://github.com/EBISPOT/clyh_ontology
 products:
   - id: clyh.owl

ontology/cmo.md

@@ -10,7 +10,9 @@ license:
   url: http://creativecommons.org/publicdomain/zero/1.0/
   label: CC0 1.0
 description: Morphological and physiological measurement records generated from clinical and model organism research and health programs.
-domain: clinical
+domain: health
+tags:
+  - clinical
 homepage: http://rgd.mcw.edu/rgdweb/ontology/search.html
 tracker: https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology/issues
 page: https://download.rgd.mcw.edu/ontology/clinical_measurement/

ontology/colao.md

@@ -8,7 +8,9 @@ contact:
   github: JCGiron
   orcid: 0000-0002-0851-6883
 description: "The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research. It has been built using the Ontology Develoment Kit, with the Ontology for the Anatomy of the Insect Skeleto-Muscular system (AISM) as a backbone."
-domain: Insect Anatomy.
+domain: anatomy and development
+tags:
+  - insect anatomy
 homepage: https://github.com/insect-morphology/colao
 products:
   - id: colao.owl

ontology/cro.md

@@ -3,7 +3,9 @@ layout: ontology_detail
 id: cro
 title: Contributor Role Ontology
 description: A 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.
-domain: scholarly contribution roles
+domain: information
+tags:
+  - scholarly contribution roles
 homepage: https://github.com/data2health/contributor-role-ontology
 tracker: https://github.com/data2health/contributor-role-ontology/issues
 contact:

ontology/cteno.md

@@ -16,7 +16,7 @@ contact:
   github: cmungall
   orcid: 0000-0002-6601-2165
 description: An anatomical and developmental ontology for ctenophores (Comb Jellies)
-domain: anatomy
+domain: anatomy and development
 homepage: https://github.com/obophenotype/ctenophore-ontology
 products:
   - id: cteno.owl

ontology/ddanat.md

@@ -7,7 +7,7 @@ contact:
   github: pfey03
   orcid: 0000-0002-4532-2703
 description: A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum
-domain: anatomy
+domain: anatomy and development
 homepage: http://dictybase.org/
 twitter: dictybase
 license:

ontology/ddpheno.md

@@ -10,7 +10,7 @@ license:
   url: http://creativecommons.org/publicdomain/zero/1.0/
   label: CC0 1.0
 description: A structured controlled vocabulary of phenotypes of the slime-mould <i>Dictyostelium discoideum</i>.
-domain: anatomy
+domain: anatomy and development
 homepage: http://dictybase.org/
 tracker: https://github.com/obophenotype/dicty-phenotype-ontology/issues
 twitter: dictybase

ontology/disdriv.md

@@ -8,7 +8,9 @@ contact:
   orcid: 0000-0001-8910-9851
 description: Ontology for drivers and triggers of human diseases, built to classify ExO ontology exposure stressors. An application ontology. Built in collaboration with EnvO, ExO, ECTO and ChEBI.
 twitter: diseaseontology
-domain: disease
+domain: health
+tags:
+  - disease
 homepage: http://www.disease-ontology.org
 products:
   - id: disdriv.owl

ontology/doid.md

@@ -9,7 +9,9 @@ contact:
   orcid: 0000-0001-8910-9851
 description: An ontology for describing the classification of human diseases organized by etiology.
 twitter: diseaseontology
-domain: disease
+domain: health
+tags:
+  - disease
 homepage: http://www.disease-ontology.org
 products:
   - id: doid.owl

ontology/ecao.md

@@ -12,7 +12,7 @@ contact:
   github: ettensohn
   orcid: 0000-0002-3625-0955
 description: An ontology for the development and anatomy of the different species of the phylum Echinodermata (NCBITaxon:7586).
-domain: anatomy
+domain: anatomy and development
 homepage: https://github.com/echinoderm-ontology/ecao_ontology
 products:
   - id: ecao.owl

ontology/eco.md

@@ -2,7 +2,7 @@
 layout: ontology_detail
 id: eco
 description: An ontology for experimental and other evidence statements.
-domain: experiments
+domain: investigations
 homepage: https://github.com/evidenceontology/evidenceontology/
 tracker: https://github.com/evidenceontology/evidenceontology/issues
 products:

ontology/ecocore.md

@@ -15,7 +15,10 @@ contact:
   github: pbuttigieg
   orcid: 0000-0002-4366-3088
 description: Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms.
-domain: ecological functions, ecological interactions
+domain: environment
+tags:
+  - ecological functions
+  - ecological interactions
 homepage: https://github.com/EcologicalSemantics/ecocore
 products:
   - id: ecocore.owl

ontology/ehdaa2.md

@@ -9,7 +9,7 @@ license:
   label: CC BY 4.0
 description: A structured controlled vocabulary of stage-specific anatomical structures of the developing human.
 tracker: https://github.com/obophenotype/human-developmental-anatomy-ontology/issues
-domain: anatomy
+domain: anatomy and development
 homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology
 products:
   - id: ehdaa2.owl

ontology/emap.md

@@ -7,7 +7,7 @@ contact:
   github: tfhayamizu
   orcid: 0000-0002-0956-8634
 description: A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus).
-domain: anatomy
+domain: anatomy and development
 homepage: http://emouseatlas.org
 page: https://www.emouseatlas.org/emap/about/what_is_emap.html
 products:

ontology/emapa.md

@@ -10,7 +10,7 @@ license:
   url: https://creativecommons.org/licenses/by/4.0/
   label: CC BY 4.0
 description: "An ontology for mouse anatomy covering embryonic development and postnatal stages."
-domain: anatomy
+domain: anatomy and development
 homepage: http://www.informatics.jax.org/expression.shtml
 tracker: https://github.com/obophenotype/mouse-anatomy-ontology/issues
 products:

ontology/epio.md

@@ -4,7 +4,9 @@ id: epio
 label: Epilepsy Ontology
 title: Epilepsy Ontology
 description: A application driven Epilepsy Ontology with official terms from the ILAE.
-domain: disease
+domain: health
+tags:
+  - disease
 license:
   url: http://creativecommons.org/licenses/by/4.0/
   label: CC BY 4.0

ontology/ero.md

@@ -8,7 +8,9 @@ license:
   url: https://creativecommons.org/licenses/by/2.0/
   label: CC BY 2.0
 description: An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens.
-domain: resources
+domain: information
+tags:
+  - resources
 homepage: https://open.med.harvard.edu/wiki/display/eaglei/Ontology
 documentation: https://open.med.harvard.edu/wiki/display/eaglei/Ontology
 products:

ontology/eupath.md

@@ -10,7 +10,12 @@ license:
   url: http://creativecommons.org/licenses/by/4.0/
   label: CC BY 4.0
 depicted_by: https://raw.githubusercontent.com/EuPathDB/communitysite/master/assets/images/VEuPathDB-logo-s.png
-domain: functional genomics, population biology, clinical epidemiology, and microbiomes
+domain: organisms
+tags:
+  - functional genomics
+  - population biology
+  - clinical epidemiology
+  - microbiomes
 description: An ontology is developed to support Eukaryotic Pathogen, Host & Vector Genomics Resource (VEuPathDB; https://veupathdb.org).
 homepage: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology
 products:

ontology/fao.md

@@ -10,7 +10,7 @@ license:
   url: http://creativecommons.org/publicdomain/zero/1.0/
   label: CC0 1.0
 description: A structured controlled vocabulary for the anatomy of fungi.
-domain: anatomy
+domain: anatomy and development
 tracker: https://github.com/obophenotype/fungal-anatomy-ontology/issues
 homepage: https://github.com/obophenotype/fungal-anatomy-ontology/
 products:

ontology/fbbi.md

@@ -11,7 +11,9 @@ license:
   url: https://creativecommons.org/licenses/by/4.0/
   label: CC BY 4.0
 description: A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.
-domain: imaging experiments
+domain: investigations
+tags:
+  - imaging experiments
 homepage: http://cellimagelibrary.org/
 tracker: https://github.com/CRBS/Biological_Imaging_Methods_Ontology/issues
 products:

ontology/fbbt.md

@@ -8,7 +8,9 @@ contact:
   github: Clare72
   orcid: 0000-0002-1373-1705
 description: An ontology representing the gross anatomy of Drosophila melanogaster.
-domain: Drosophilid anatomy
+domain: anatomy and development
+tags:
+  - Drosophilid anatomy
 homepage: http://purl.obolibrary.org/obo/fbbt
 repository: https://github.com/FlyBase/drosophila-anatomy-developmental-ontology
 products:

ontology/fbdv.md

@@ -8,7 +8,7 @@ contact:
   github: Clare72
   orcid: 0000-0002-1373-1705
 description: A structured controlled vocabulary of the development of Drosophila melanogaster.
-domain: development
+domain: anatomy and development
 homepage: http://purl.obolibrary.org/obo/fbdv
 repository: https://github.com/FlyBase/drosophila-developmental-ontology
 products:

ontology/fbsp.md

@@ -7,7 +7,9 @@ contact:
   github: Clare72
   orcid: 0000-0002-1373-1705
 description: The taxonomy of the family <i>Drosophilidae</i> (largely after Baechli) and of other taxa referred to in FlyBase.
-domain: taxonomy
+domain: organisms
+tags:
+  - taxonomy
 homepage: http://www.flybase.org/
 products:
   - id: fbsp.owl

ontology/fideo.md

@@ -3,7 +3,7 @@ layout: ontology_detail
 id: fideo
 title: Food Interactions with Drugs Evidence Ontology
 description: Food-Drug interactions automatically extracted from scientific literature
-domain: diet, metabolomics and nutrition
+domain: diet, metabolomics, and nutrition
 homepage: https://gitub.u-bordeaux.fr/erias/fideo
 contact:
   email: [email protected]

ontology/fma.md

@@ -8,7 +8,7 @@ license:
   url: https://creativecommons.org/licenses/by/3.0/
   label: CC BY 3.0
 description: This is currently a slimmed down version of FMA
-domain: anatomy
+domain: anatomy and development
 homepage: http://si.washington.edu/projects/fma
 page: http://en.wikipedia.org/wiki/Foundational_Model_of_Anatomy
 publications:

ontology/fobi.md

@@ -7,7 +7,7 @@ contact:
   github: pcastellanoescuder
   orcid: 0000-0001-6466-877X
 description: FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data
-domain: metabolomics and nutrition
+domain: diet, metabolomics, and nutrition
 license:
   url: http://creativecommons.org/licenses/by/3.0/
   label: CC BY 3.0

ontology/foodon.md

@@ -7,7 +7,9 @@ contact:
   github: ddooley
   orcid: 0000-0002-8844-9165
 description: A broadly scoped ontology representing entities which bear a “food role”. It encompasses materials in natural ecosystems and agriculture that are consumed by humans and domesticated animals. This includes any generic (unbranded) raw or processed food material found in processing plants, markets, stores or food distribution points. FoodOn also imports nutritional component and dietary pattern terms from other OBO Foundry ontologies to support interoperability in diet and nutrition research
-domain: food
+domain: diet, metabolomics, and nutrition
+tags:
+  - food
 homepage: https://foodon.org/
 license:
   url: http://creativecommons.org/licenses/by/3.0/