Ensure dependencies are sorted (OBOFoundry#1983)

* Add tests for sorted and unique dependencies * Add stub script for sorting dependencies * Standardize dependency order * Remove duplicate dependency
cthoyt · Jul 11, 2022 · f457529 · f457529
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diff --git a/ontology/agro.md b/ontology/agro.md
@@ -12,18 +12,18 @@ contact:
   label: Marie-Angélique Laporte
   orcid: 0000-0002-8461-9745
 dependencies:
+- id: bfo
 - id: envo
-- id: go
 - id: foodon
+- id: go
+- id: iao
 - id: ncbitaxon
+- id: obi
 - id: pato
 - id: peco
 - id: po
-- id: to
 - id: ro
-- id: bfo
-- id: iao
-- id: obi
+- id: to
 - id: uo
 - id: xco
 description: Ontology of agronomic practices, agronomic techniques, and agronomic variables used in agronomic experiments

diff --git a/ontology/aism.md b/ontology/aism.md
@@ -12,12 +12,12 @@ contact:
   label: Jennifer C. Girón
   orcid: 0000-0002-0851-6883
 dependencies:
-- id: ro
-- id: uberon
-- id: caro
-- id: pato
 - id: bfo
 - id: bspo
+- id: caro
+- id: pato
+- id: ro
+- id: uberon
 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

diff --git a/ontology/cdno.md b/ontology/cdno.md
@@ -12,11 +12,11 @@ contact:
   label: Liliana Andres Hernandez
   orcid: 0000-0002-7696-731X
 dependencies:
-- id: ro
 - id: bfo
-- id: pato
 - id: chebi
 - id: envo
+- id: pato
+- id: ro
 description: CDNO provides structured terminologies to describe nutritional attributes of material entities that contribute to human diet.
 domain: diet, metabolomics, and nutrition
 homepage: https://cdno.info/

diff --git a/ontology/chiro.md b/ontology/chiro.md
@@ -13,12 +13,12 @@ contact:
   orcid: 0000-0001-5208-3432
 dependencies:
 - id: chebi
-- id: mp
-- id: hp
 - id: go
+- id: hp
+- id: mp
+- id: ncbitaxon
 - id: pr
 - id: uberon
-- id: ncbitaxon
 description: CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes.
 domain: chemistry and biochemistry
 homepage: https://github.com/obophenotype/chiro

diff --git a/ontology/cl.md b/ontology/cl.md
@@ -15,13 +15,13 @@ contact:
   label: Alexander Diehl
   orcid: 0000-0001-9990-8331
 dependencies:
-- id: uberon
-- id: go
-- id: ro
 - id: chebi
+- id: go
+- id: ncbitaxon
 - id: pato
 - id: pr
-- id: ncbitaxon
+- id: ro
+- id: uberon
 description: The Cell Ontology is a structured controlled vocabulary for cell types in animals.
 domain: anatomy and development
 homepage: https://obophenotype.github.io/cell-ontology/

diff --git a/ontology/clo.md b/ontology/clo.md
@@ -8,10 +8,10 @@ contact:
   label: Sirarat Sarntivijai
   orcid: 0000-0002-2548-641X
 dependencies:
-- id: uberon
 - id: cl
 - id: doid
 - id: ncbitaxon
+- id: uberon
 description: An ontology to standardize and integrate cell line information and to support computer-assisted reasoning.
 domain: anatomy and development
 homepage: http://www.clo-ontology.org

diff --git a/ontology/clyh.md b/ontology/clyh.md
@@ -12,9 +12,9 @@ contact:
   label: Lucas Leclere
   orcid: 0000-0002-7440-0467
 dependencies:
-- id: uberon
-- id: ro
 - id: iao
+- id: ro
+- id: uberon
 description: The Clytia hemisphaerica Development and Anatomy Ontology (CLYH) describes the anatomical and developmental features of the Clytia hemisphaerica life cycle.
 domain: anatomy and development
 homepage: https://github.com/EBISPOT/clyh_ontology

diff --git a/ontology/colao.md b/ontology/colao.md
@@ -9,12 +9,12 @@ contact:
   orcid: 0000-0002-0851-6883
 dependencies:
 - id: aism
-- id: ro
-- id: uberon
-- id: caro
-- id: pato
 - id: bfo
 - id: bspo
+- id: caro
+- id: pato
+- id: ro
+- id: uberon
 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: anatomy and development
 homepage: https://github.com/insect-morphology/colao

diff --git a/ontology/cteno.md b/ontology/cteno.md
@@ -13,8 +13,8 @@ contact:
   label: Chris Mungall
   orcid: 0000-0002-6601-2165
 dependencies:
-- id: uberon
 - id: ro
+- id: uberon
 description: An anatomical and developmental ontology for ctenophores (Comb Jellies)
 domain: anatomy and development
 homepage: https://github.com/obophenotype/ctenophore-ontology

diff --git a/ontology/duo.md b/ontology/duo.md
@@ -12,8 +12,8 @@ contact:
   label: Melanie Courtot
   orcid: 0000-0002-9551-6370
 dependencies:
-- id: iao
 - id: bfo
+- id: iao
 description: DUO is an ontology which represent data use conditions.
 domain: information
 homepage: https://github.com/EBISPOT/DUO

diff --git a/ontology/ecao.md b/ontology/ecao.md
@@ -12,9 +12,9 @@ contact:
   label: Charles Ettensohn
   orcid: 0000-0002-3625-0955
 dependencies:
-- id: uberon
-- id: ro
 - id: cl
+- id: ro
+- id: uberon
 description: An ontology for the development and anatomy of the different species of the phylum Echinodermata (NCBITaxon:7586).
 domain: anatomy and development
 homepage: https://github.com/echinoderm-ontology/ecao_ontology

diff --git a/ontology/ecocore.md b/ontology/ecocore.md
@@ -12,16 +12,16 @@ contact:
   label: Pier Luigi Buttigieg
   orcid: 0000-0002-4366-3088
 dependencies:
-- id: pco
-- id: ro
 - id: bfo
-- id: pato
-- id: envo
 - id: chebi
+- id: envo
 - id: go
-- id: uberon
-- id: po
 - id: iao
+- id: pato
+- id: pco
+- id: po
+- id: ro
+- id: uberon
 description: Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms.
 domain: environment
 homepage: https://github.com/EcologicalSemantics/ecocore

diff --git a/ontology/ecto.md b/ontology/ecto.md
@@ -19,8 +19,8 @@ dependencies:
 - id: iao
 - id: maxo
 - id: nbo
-- id: ncit
 - id: ncbitaxon
+- id: ncit
 - id: pato
 - id: ro
 - id: uberon

diff --git a/ontology/envo.md b/ontology/envo.md
@@ -15,14 +15,14 @@ contact:
   label: Pier Luigi Buttigieg
   orcid: 0000-0002-4366-3088
 dependencies:
-- id: uberon
-- id: pco
-- id: ro
 - id: chebi
-- id: ncbitaxon
 - id: foodon
-- id: po
 - id: go
+- id: ncbitaxon
+- id: pco
+- id: po
+- id: ro
+- id: uberon
 depicted_by: /logos/envo.png
 description: Ontology of environmental features and habitats
 domain: environment

diff --git a/ontology/foodon.md b/ontology/foodon.md
@@ -8,14 +8,14 @@ contact:
   label: Damion Dooley
   orcid: 0000-0002-8844-9165
 dependencies:
-- id: uberon
-- id: ro
-- id: eo
-- id: chebi
-- id: ncbitaxon
 - id: bfo
+- id: chebi
 - id: envo
+- id: eo
+- id: ncbitaxon
 - id: obi
+- id: ro
+- id: uberon
 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: diet, metabolomics, and nutrition
 homepage: https://foodon.org/

diff --git a/ontology/fovt.md b/ontology/fovt.md
@@ -13,12 +13,12 @@ contact:
   orcid: 0000-0003-2699-3066
 dependencies:
 - id: bco
-- id: oba
-- id: ro
 - id: bfo
-- id: pato
 - id: bspo
 - id: iao
+- id: oba
+- id: pato
+- id: ro
 - id: uberon
 description: FuTRES Ontology of Vertebrate Traits is an application ontology used to convert vertebrate trait data in spreadsheet to triples. FOVT leverages the BioCollections Ontology (BCO) to link observations of individual specimens to their trait values. Traits are defined in the Ontology of Biological Attributes (OBA).
 domain: phenotype

diff --git a/ontology/genepio.md b/ontology/genepio.md
@@ -8,11 +8,11 @@ contact:
   label: Damion Dooley
   orcid: 0000-0002-8844-9165
 dependencies:
-- id: uberon
-- id: po
-- id: ro
 - id: chebi
 - id: ncbitaxon
+- id: po
+- id: ro
+- id: uberon
 description: The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks.
 domain: health
 homepage: http://genepio.org/

diff --git a/ontology/go.md b/ontology/go.md
@@ -12,14 +12,8 @@ contact:
   label: Suzi Aleksander
   orcid: 0000-0001-6787-2901
 dependencies:
-- id: uberon
-  subset: go/extensions/uberon_import.owl
 - id: cl
   subset: go/extensions/cl_import.owl
-- id: ncbitaxon
-  subset: go/extensions/ncbitaxon_import.owl
-- id: ro
-  subset: go/extensions/ro_import.owl
 - id: go/extensions/go-bridge-to-nifstd.owl
   title: GO bridge to NIFSTD
   connects:
@@ -30,6 +24,12 @@ dependencies:
   - id: http://www.ncbi.nlm.nih.gov/pubmed/24093723
     title: 'The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments.'
   type: BridgeOntology
+- id: ncbitaxon
+  subset: go/extensions/ncbitaxon_import.owl
+- id: ro
+  subset: go/extensions/ro_import.owl
+- id: uberon
+  subset: go/extensions/uberon_import.owl
 depicted_by: http://geneontology.org/assets/go-logo-icon.mini.png
 description: An ontology for describing the function of genes and gene products
 domain: biological systems

diff --git a/ontology/hso.md b/ontology/hso.md
@@ -8,11 +8,11 @@ contact:
   label: Fernanda Dorea
   orcid: 0000-0001-8638-8525
 dependencies:
-- id: uberon
 - id: bfo
-- id: ro
-- id: obi
 - id: ncbitaxon
+- id: obi
+- id: ro
+- id: uberon
 description: The health Surveillance Ontology (HSO) focuses on "surveillance system level data", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance.
 domain: health
 homepage: https://w3id.org/hso

diff --git a/ontology/lepao.md b/ontology/lepao.md
@@ -9,12 +9,12 @@ contact:
   orcid: 0000-0002-9136-9932
 dependencies:
 - id: aism
-- id: ro
-- id: uberon
-- id: caro
-- id: pato
 - id: bfo
 - id: bspo
+- id: caro
+- id: pato
+- id: ro
+- id: uberon
 description: The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research. LEPAO is developed in part by BIOfid (The Specialised Information Service Biodiversity Research).
 domain: anatomy and development
 homepage: https://github.com/insect-morphology/lepao

diff --git a/ontology/maxo.md b/ontology/maxo.md
@@ -12,12 +12,12 @@ contact:
   label: Leigh Carmody
   orcid: 0000-0001-7941-2961
 dependencies:
-- id: iao
+- id: chebi
+- id: foodon
 - id: go
+- id: iao
 - id: ro
 - id: uberon
-- id: foodon
-- id: chebi
 depicted_by: https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/maxo-logos/maxo_logo_black-banner.png
 description: Medical Action Ontology is an ontology...
 domain: health

diff --git a/ontology/mco.md b/ontology/mco.md
@@ -18,12 +18,12 @@ dependencies:
 - id: clo
 - id: micro
 - id: ncbitaxon
-- id: peco
 - id: ncit
 - id: obi
 - id: omit
 - id: omp
 - id: pato
+- id: peco
 - id: uberon
 - id: zeco
 description: Microbial Conditions Ontology is an ontology...

diff --git a/ontology/one.md b/ontology/one.md
@@ -8,9 +8,9 @@ contact:
   label: Chen Yang
   orcid: 0000-0001-9202-5309
 dependencies:
-- id: ons
-- id: obi
 - id: foodon
+- id: obi
+- id: ons
 description: An ontology to standardize research output of nutritional epidemiologic studies.
 domain: diet, metabolomics, and nutrition
 homepage: https://github.com/cyang0128/Nutritional-epidemiologic-ontologies

diff --git a/ontology/ons.md b/ontology/ons.md
@@ -8,14 +8,14 @@ contact:
   label: Francesco Vitali
   orcid: 0000-0001-9125-4337
 dependencies:
-- id: uberon
-- id: ro
-- id: chebi
-- id: ncbitaxon
 - id: bfo
+- id: chebi
 - id: envo
-- id: obi
 - id: foodon
+- id: ncbitaxon
+- id: obi
+- id: ro
+- id: uberon
 description: An ontology for description of concepts in the nutritional studies domain.
 domain: diet, metabolomics, and nutrition
 homepage: https://github.com/enpadasi/Ontology-for-Nutritional-Studies

diff --git a/ontology/ontoavida.md b/ontology/ontoavida.md
@@ -10,9 +10,9 @@ contact:
 dependencies:
 - id: fbcv
 - id: gsso
-- id: stato
-- id: ro
 - id: ncit
+- id: ro
+- id: stato
 description: OntoAvida develops an integrated vocabulary for the description of the most widely-used computational approach for studying evolution using digital organisms (i.e., self-replicating computer programs that evolve within a user-defined computational environment).
 domain: simulation
 homepage: https://gitlab.com/fortunalab/ontoavida