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Standardize YAML in ontology metadata frontmatter (#1985)
* Standardize YAML in ontology metadata frontmatter This PR does the following: 1. Introduces a Python script util/standardize_metadata.py that sorts and properly indents all of the metadata in all ontology metadata files' frontmatter 2. Adds a unit test to ensure that this metadata is sorted Why do this? It makes it much easier to programatically edit these files without creating massive diffs (after the massive diff in this PR, at least). There are several ways we might want to automatically maintain these metadata, such as the list of dependencies for each ontology. * Update tox.ini * Update aao.md * Update test_integrity.py * Modify dumping procedure * Cleanup * Set up package for code reuse * Update config.yamllint * Add extra examples * Update standardize_metadata.py * Cleanup * Update setup.cfg
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@@ -5,12 +5,12 @@ title: Amphibian gross anatomy | |
| contact: | ||
| email: [email protected] | ||
| label: David Blackburn | ||
| taxon: | ||
| id: NCBITaxon:8292 | ||
| label: Amphibia | ||
| homepage: http://github.com/seger/aao | ||
| is_obsolete: true | ||
| replaced_by: uberon | ||
| taxon: | ||
| id: NCBITaxon:8292 | ||
| label: Amphibia | ||
| activity_status: inactive | ||
| --- | ||
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@@ -4,22 +4,22 @@ id: ado | |
| title: Alzheimer's Disease Ontology | ||
| contact: | ||
| email: [email protected] | ||
| label: Alpha Tom Kodamullil | ||
| github: akodamullil | ||
| label: Alpha Tom Kodamullil | ||
| orcid: 0000-0001-9896-3531 | ||
| dependencies: | ||
| - id: bfo | ||
| description: Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelated entities that demonstrate the network of the understanding on Alzheimer's disease and can be readily applied for text mining. | ||
| domain: health | ||
| homepage: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO | ||
| products: | ||
| - id: ado.owl | ||
| dependencies: | ||
| - id: bfo | ||
| tracker: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO/issues | ||
| license: | ||
| url: https://creativecommons.org/licenses/by/4.0/ | ||
| label: CC BY 4.0 | ||
| repository: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO | ||
| url: https://creativecommons.org/licenses/by/4.0/ | ||
| preferredPrefix: ADO | ||
| products: | ||
| - id: ado.owl | ||
| repository: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO | ||
| tracker: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO/issues | ||
| activity_status: active | ||
| --- | ||
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| @@ -1,27 +1,27 @@ | ||
| --- | ||
| layout: ontology_detail | ||
| id: aeo | ||
| title: Anatomical Entity Ontology | ||
| build: | ||
| checkout: git clone https://github.com/obophenotype/human-developmental-anatomy-ontology.git | ||
| method: vcs | ||
| path: src/ontology | ||
| system: git | ||
| contact: | ||
| email: [email protected] | ||
| label: Jonathan Bard | ||
| 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 and development | ||
| homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology/ | ||
| tracker: https://github.com/obophenotype/human-developmental-anatomy-ontology/issues | ||
| license: | ||
| label: CC BY 4.0 | ||
| url: https://creativecommons.org/licenses/by/4.0/ | ||
| preferredPrefix: AEO | ||
| products: | ||
| - id: aeo.owl | ||
| title: Anatomical Entity Ontology | ||
| build: | ||
| checkout: git clone https://github.com/obophenotype/human-developmental-anatomy-ontology.git | ||
| system: git | ||
| path: src/ontology | ||
| method: vcs | ||
| activity_status: inactive | ||
| - id: aeo.owl | ||
| repository: https://github.com/obophenotype/human-developmental-anatomy-ontology | ||
| preferredPrefix: AEO | ||
| tracker: https://github.com/obophenotype/human-developmental-anatomy-ontology/issues | ||
| activity_status: inactive | ||
| --- | ||
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| 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 | ||
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| @@ -1,23 +1,23 @@ | ||
| --- | ||
| layout: ontology_detail | ||
| id: aero | ||
| title: Adverse Event Reporting Ontology | ||
| build: | ||
| method: owl2obo | ||
| source_url: http://purl.obolibrary.org/obo/aero.owl | ||
| contact: | ||
| orcid: 0000-0002-9551-6370 | ||
| email: [email protected] | ||
| label: Melanie Courtot | ||
| orcid: 0000-0002-9551-6370 | ||
| description: The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events | ||
| license: | ||
| url: http://creativecommons.org/licenses/by/3.0/ | ||
| label: CC BY 3.0 | ||
| domain: health | ||
| homepage: http://purl.obolibrary.org/obo/aero | ||
| is_obsolete: true | ||
| license: | ||
| label: CC BY 3.0 | ||
| url: http://creativecommons.org/licenses/by/3.0/ | ||
| products: | ||
| - id: aero.owl | ||
| title: Adverse Event Reporting Ontology | ||
| build: | ||
| source_url: http://purl.obolibrary.org/obo/aero.owl | ||
| method: owl2obo | ||
| - id: aero.owl | ||
| activity_status: inactive | ||
| --- | ||
|
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@@ -2,57 +2,57 @@ | |
| layout: ontology_detail | ||
| id: agro | ||
| title: Agronomy Ontology | ||
| license: | ||
| url: https://creativecommons.org/licenses/by/4.0/ | ||
| label: CC BY 4.0 | ||
| domain: agriculture | ||
| tags: | ||
| - agronomy | ||
| build: | ||
| checkout: git clone https://github.com/AgriculturalSemantics/agro.git | ||
| path: . | ||
| system: git | ||
| path: "." | ||
| description: Ontology of agronomic practices, agronomic techniques, and agronomic variables used in agronomic experiments | ||
| homepage: https://github.com/AgriculturalSemantics/agro | ||
| contact: | ||
| email: [email protected] | ||
| github: marieALaporte | ||
| label: Marie-Angélique Laporte | ||
| github: "marieALaporte" | ||
| orcid: 0000-0002-8461-9745 | ||
| dependencies: | ||
| - id: envo | ||
| - id: go | ||
| - id: foodon | ||
| - id: ncbitaxon | ||
| - id: pato | ||
| - id: peco | ||
| - id: po | ||
| - id: to | ||
| - id: ro | ||
| - id: bfo | ||
| - id: iao | ||
| - id: obi | ||
| - id: uo | ||
| - id: xco | ||
| description: Ontology of agronomic practices, agronomic techniques, and agronomic variables used in agronomic experiments | ||
| domain: agriculture | ||
| homepage: https://github.com/AgriculturalSemantics/agro | ||
| jobs: | ||
| - id: https://travis-ci.org/AgriculturalSemantics/agro | ||
| type: travis-ci | ||
| license: | ||
| label: CC BY 4.0 | ||
| url: https://creativecommons.org/licenses/by/4.0/ | ||
| preferredPrefix: AGRO | ||
| products: | ||
| - id: agro.owl | ||
| title: "AgrO" | ||
| description: "Contains all AgrO terms and links to other relavent ontologies." | ||
| - id: agro.owl | ||
| title: AgrO | ||
| description: Contains all AgrO terms and links to other relavent ontologies. | ||
| publications: | ||
| - id: http://ceur-ws.org/Vol-1747/IT205_ICBO2016.pdf | ||
| title: "Data-driven Agricultural Research for Development: A Need for Data Harmonization Via Semantics." | ||
| usages: | ||
| - user: https://agrofims.org/about | ||
| description: AgroFIMS enables digital collection of agronomic data that is semantically described a priori with agronomic terms from AgrO. | ||
| - user: https://gardian.bigdata.cgiar.org/ | ||
| description: AgrO is being used by GARDIAN to facilitate data search within publications and datasets for use in quantitative analyses. | ||
| jobs: | ||
| - id: https://travis-ci.org/AgriculturalSemantics/agro | ||
| type: travis-ci | ||
| - id: http://ceur-ws.org/Vol-1747/IT205_ICBO2016.pdf | ||
| title: 'Data-driven Agricultural Research for Development: A Need for Data Harmonization Via Semantics.' | ||
| repository: https://github.com/AgriculturalSemantics/agro | ||
| tags: | ||
| - agronomy | ||
| tracker: https://github.com/AgriculturalSemantics/agro/issues/ | ||
| usages: | ||
| - description: AgroFIMS enables digital collection of agronomic data that is semantically described a priori with agronomic terms from AgrO. | ||
| user: https://agrofims.org/about | ||
| - description: AgrO is being used by GARDIAN to facilitate data search within publications and datasets for use in quantitative analyses. | ||
| user: https://gardian.bigdata.cgiar.org/ | ||
| activity_status: active | ||
| repository: https://github.com/AgriculturalSemantics/agro | ||
| dependencies: | ||
| - id: envo | ||
| - id: go | ||
| - id: foodon | ||
| - id: ncbitaxon | ||
| - id: pato | ||
| - id: peco | ||
| - id: po | ||
| - id: to | ||
| - id: ro | ||
| - id: bfo | ||
| - id: iao | ||
| - id: obi | ||
| - id: uo | ||
| - id: xco | ||
| preferredPrefix: AGRO | ||
| --- | ||
|
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| 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. | ||
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@@ -4,32 +4,32 @@ id: aism | |
| title: Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) | ||
| build: | ||
| checkout: git clone https://github.com/insect-morphology/aism | ||
| path: . | ||
| system: git | ||
| path: "." | ||
| contact: | ||
| email: [email protected] | ||
| label: Jennifer C. Girón | ||
| github: JCGiron | ||
| label: Jennifer C. Girón | ||
| orcid: 0000-0002-0851-6883 | ||
| dependencies: | ||
| - id: ro | ||
| - id: uberon | ||
| - id: caro | ||
| - id: pato | ||
| - id: bfo | ||
| - id: bspo | ||
| 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 and development | ||
| homepage: https://github.com/insect-morphology/aism | ||
| products: | ||
| - id: aism.owl | ||
| - id: aism.obo | ||
| - id: aism.json | ||
| dependencies: | ||
| - id: ro | ||
| - id: uberon | ||
| - id: caro | ||
| - id: pato | ||
| - id: bfo | ||
| - id: bspo | ||
| tracker: https://github.com/insect-morphology/aism/issues | ||
| license: | ||
| url: https://creativecommons.org/licenses/by/4.0/ | ||
| label: CC BY 4.0 | ||
| activity_status: active | ||
| repository: https://github.com/insect-morphology/aism | ||
| url: https://creativecommons.org/licenses/by/4.0/ | ||
| preferredPrefix: AISM | ||
| products: | ||
| - id: aism.owl | ||
| - id: aism.obo | ||
| - id: aism.json | ||
| repository: https://github.com/insect-morphology/aism | ||
| tracker: https://github.com/insect-morphology/aism/issues | ||
| activity_status: active | ||
| --- | ||
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@@ -4,28 +4,28 @@ id: amphx | |
| title: The Amphioxus Development and Anatomy Ontology | ||
| build: | ||
| checkout: git clone https://github.com/EBISPOT/amphx_ontology.git | ||
| path: . | ||
| system: git | ||
| path: "." | ||
| contact: | ||
| email: [email protected] | ||
| label: Hector Escriva | ||
| github: hescriva | ||
| label: Hector Escriva | ||
| orcid: 0000-0001-7577-5028 | ||
| dependencies: | ||
| - id: uberon | ||
| description: An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum). | ||
| domain: anatomy and development | ||
| homepage: https://github.com/EBISPOT/amphx_ontology | ||
| products: | ||
| - id: amphx.owl | ||
| - id: amphx.obo | ||
| dependencies: | ||
| - id: uberon | ||
| tracker: https://github.com/EBISPOT/amphx_ontology/issues | ||
| license: | ||
| url: http://creativecommons.org/licenses/by/3.0/ | ||
| label: CC BY 3.0 | ||
| activity_status: active | ||
| repository: https://github.com/EBISPOT/amphx_ontology | ||
| url: http://creativecommons.org/licenses/by/3.0/ | ||
| preferredPrefix: AMPHX | ||
| products: | ||
| - id: amphx.owl | ||
| - id: amphx.obo | ||
| repository: https://github.com/EBISPOT/amphx_ontology | ||
| tracker: https://github.com/EBISPOT/amphx_ontology/issues | ||
| activity_status: active | ||
| --- | ||
|
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| 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). | ||
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| @@ -1,32 +1,32 @@ | ||
| --- | ||
| layout: ontology_detail | ||
| id: apo | ||
| title: Ascomycete phenotype ontology | ||
| build: | ||
| method: obo2owl | ||
| source_url: https://raw.githubusercontent.com/obophenotype/ascomycete-phenotype-ontology/master/apo.obo | ||
| contact: | ||
| email: [email protected] | ||
| label: Stacia R Engel | ||
| github: srengel | ||
| label: Stacia R Engel | ||
| orcid: 0000-0001-5472-917X | ||
| tracker: https://github.com/obophenotype/ascomycete-phenotype-ontology/issues | ||
| license: | ||
| url: https://creativecommons.org/licenses/by/4.0/ | ||
| label: CC BY 4.0 | ||
| description: A structured controlled vocabulary for the phenotypes of Ascomycete fungi | ||
| domain: phenotype | ||
| homepage: http://www.yeastgenome.org/ | ||
| license: | ||
| label: CC BY 4.0 | ||
| url: https://creativecommons.org/licenses/by/4.0/ | ||
| preferredPrefix: APO | ||
| products: | ||
| - id: apo.owl | ||
| - id: apo.obo | ||
| - id: apo.owl | ||
| - id: apo.obo | ||
| publications: | ||
| - id: https://www.ncbi.nlm.nih.gov/pubmed/20157474 | ||
| title: New mutant phenotype data curation system in the Saccharomyces Genome Database | ||
| repository: https://github.com/obophenotype/ascomycete-phenotype-ontology | ||
| taxon: | ||
| id: NCBITaxon:4890 | ||
| label: Ascomycota | ||
| title: Ascomycete phenotype ontology | ||
| build: | ||
| source_url: https://raw.githubusercontent.com/obophenotype/ascomycete-phenotype-ontology/master/apo.obo | ||
| method: obo2owl | ||
| tracker: https://github.com/obophenotype/ascomycete-phenotype-ontology/issues | ||
| activity_status: active | ||
| repository: https://github.com/obophenotype/ascomycete-phenotype-ontology | ||
| preferredPrefix: APO | ||
| publications: | ||
| - id: https://www.ncbi.nlm.nih.gov/pubmed/20157474 | ||
| title: "New mutant phenotype data curation system in the Saccharomyces Genome Database" | ||
| --- |
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