Simplify maintenance of publication list (OBOFoundry#2128)

* Use templating for listing publications * Update Makefile
LK112019 · Oct 9, 2022 · 407276d · 407276d
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diff --git a/Makefile b/Makefile
@@ -38,7 +38,7 @@ PRINCIPLES := $(wildcard principles/*.md)
 ### Main Tasks
 .PHONY: all pull_and_build test pull clean
 
-all: _config.yml registry/ontologies.ttl registry/publications.md registry/obo_context.jsonld registry/obo_prefixes.ttl
+all: _config.yml registry/ontologies.ttl registry/obo_context.jsonld registry/obo_prefixes.ttl
 
 pull:
 	git pull
@@ -51,8 +51,8 @@ integration-test: test valid-purl-report.txt
 
 # Remove and/or revert all targets to their repository versions:
 clean:
-	rm -Rf registry/ontologies.nt registry/ontologies.ttl registry/ontologies.yml registry/publications.md sparql-consistency-report.txt jenkins-output.txt valid-purl-report.txt valid-purl-report.txt.tmp _site/ tmp/ reports/
-	git checkout _config.yml registry/ontologies.jsonld registry/ontologies.ttl registry/ontologies.yml registry/publications.md
+	rm -Rf registry/ontologies.nt registry/ontologies.ttl registry/ontologies.yml sparql-consistency-report.txt jenkins-output.txt valid-purl-report.txt valid-purl-report.txt.tmp _site/ tmp/ reports/
+	git checkout _config.yml registry/ontologies.jsonld registry/ontologies.ttl registry/ontologies.yml
 
 
 ### Directories:
@@ -113,10 +113,6 @@ registry/ontologies.nt: registry/ontologies.jsonld
 registry/ontologies.ttl: registry/ontologies.nt
 	riot --base=http://purl.obolibrary.org/obo/ --out=ttl $< > $@.tmp && mv $@.tmp $@
 
-# Generate a list of primary publications
-registry/publications.md: registry/ontologies.yml
-	util/extract-publications.py $< $@
-
 ### Validate Configuration Files
 
 # generate both a report of the violations and a grid of all results

diff --git a/registry/publications.md b/registry/publications.md
@@ -2,9 +2,6 @@
 layout: doc
 title: Publications Related to the OBO Foundry
 ---
-
-[//]: <> (Do not edit this file manually, it is automatically generated by https://github.com/OBOFoundry/OBOFoundry.github.io/blob/master/util/extract-publications.py.)
-
 ## Citing the OBO Foundry
 
 [**OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies**](https://academic.oup.com/database/article/doi/10.1093/database/baab069/6410158) **(2021)**.
@@ -23,92 +20,13 @@ Barry Smith, Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug, Wer
 
 ### Some Ontology Project Publications (not a complete list)
 
-- Agronomy Ontology (agro): [Data-driven Agricultural Research for Development: A Need for Data Harmonization Via Semantics.](http://ceur-ws.org/Vol-1747/IT205_ICBO2016.pdf)
-- Antibiotic Resistance Ontology (aro): [CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database.](https://www.ncbi.nlm.nih.gov/pubmed/31665441)
-- Apollo Structured Vocabulary (apollo_sv): [The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation](https://doi.org/10.1186/s13326-016-0092-y)
-- Ascomycete phenotype ontology (apo): [New mutant phenotype data curation system in the Saccharomyces Genome Database](https://www.ncbi.nlm.nih.gov/pubmed/20157474)
-- BRENDA tissue / enzyme source (bto): [The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources](https://www.ncbi.nlm.nih.gov/pubmed/21030441)
-- Biological Spatial Ontology (bspo): [Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology.](https://www.ncbi.nlm.nih.gov/pubmed/25140222)
-- C. elegans Gross Anatomy Ontology (wbbt): [Building a cell and anatomy ontology of Caenorhabditis elegans](https://www.ncbi.nlm.nih.gov/pubmed/18629098)
-- C. elegans development ontology (wbls): [WormBase: a modern Model Organism Information Resource](https://www.ncbi.nlm.nih.gov/pubmed/31642470)
-- C. elegans phenotype (wbphenotype): [Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community.](https://www.ncbi.nlm.nih.gov/pubmed/21261995)
-- CHEBI Integrated Role Ontology (chiro): [Extension of Roles in the ChEBI Ontology](https://doi.org/10.26434/chemrxiv.12591221)
-- Cell Line Ontology (clo): [CLO: The Cell Line Ontology](https://www.ncbi.nlm.nih.gov/pubmed/25852852)
-- Cell Ontology (cl): [The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.](https://www.ncbi.nlm.nih.gov/pubmed/27377652)
-- Chemical Entities of Biological Interest (chebi): [ChEBI in 2016: Improved services and an expanding collection of metabolites.](https://www.ncbi.nlm.nih.gov/pubmed/26467479)
-- Chemical Information Ontology (cheminf): [The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web](https://www.ncbi.nlm.nih.gov/pubmed/21991315)
-- Clinical measurement ontology (cmo): [Three ontologies to define phenotype measurement data.](https://www.ncbi.nlm.nih.gov/pubmed/22654893)
-- Comparative Data Analysis Ontology (cdao): [Initial Implementation of a Comparative Data Analysis Ontology](https://doi.org/10.4137/EBO.S2320)
-- Compositional Dietary Nutrition Ontology (cdno): [Knowledge representation and data sharing to unlock crop variation for nutritional food security](https://doi.org/10.1002/csc2.20092)
-- Confidence Information Ontology (cio): [The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations](https://www.ncbi.nlm.nih.gov/pubmed/25957950)
-- Dictyostelium discoideum anatomy (ddanat): [An anatomy ontology to represent biological knowledge in Dictyostelium discoideum](https://www.ncbi.nlm.nih.gov/pubmed/18366659)
-- Dictyostelium discoideum phenotype ontology (ddpheno): [dictyBase and the Dicty Stock Center (version 2.0) - a progress report](https://www.ncbi.nlm.nih.gov/pubmed/31840793)
-- Drosophila Phenotype Ontology (dpo): [The Drosophila phenotype ontology.](https://www.ncbi.nlm.nih.gov/pubmed/24138933)
-- Drosophila gross anatomy (fbbt): [The Drosophila anatomy ontology](https://www.ncbi.nlm.nih.gov/pubmed/24139062)
-- Environment Ontology (envo): [The environment ontology: contextualising biological and biomedical entities](https://doi.org/10.1186/2041-1480-4-43)
-- Evidence ontology (eco): [ECO, the Evidence & Conclusion Ontology: community standard for evidence information.](https://www.ncbi.nlm.nih.gov/pubmed/30407590)
-- Experimental condition ontology (xco): [Three ontologies to define phenotype measurement data.](https://www.ncbi.nlm.nih.gov/pubmed/22654893)
-- Fission Yeast Phenotype Ontology (fypo): [FYPO: The Fission Yeast Phenotype Ontology.](https://www.ncbi.nlm.nih.gov/pubmed/23658422)
-- Flora Phenotype Ontology (flopo): [The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants](https://www.ncbi.nlm.nih.gov/pubmed/27842607)
-- Food Ontology (foodon): [FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration](https://www.ncbi.nlm.nih.gov/pubmed/31304272)
-- Food-Biomarker Ontology (fobi): [FOBI: an ontology to represent food intake data and associate it with metabolomic data](https://www.ncbi.nlm.nih.gov/pubmed/32556148)
-- Foundational Model of Anatomy Ontology (subset) (fma): [Translating the Foundational Model of Anatomy into OWL](https://www.ncbi.nlm.nih.gov/pubmed/18688289)
-- Gene Ontology (go): [Gene ontology: tool for the unification of biology. The Gene Ontology Consortium](https://www.ncbi.nlm.nih.gov/pubmed/10802651)
-- Glycan Naming and Subsumption Ontology (GNOme) (gno): [GNOme - Glycan Naming and Subsumption Ontology](https://doi.org/10.5281/zenodo.6678278)
-- Homology Ontology (hom): [An ontology to clarify homology-related concepts](https://doi.org/10.1016/j.tig.2009.12.012)
-- Human Ancestry Ontology (hancestro): [A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog](https://www.ncbi.nlm.nih.gov/pubmed/29448949)
-- Human Disease Ontology (doid): [Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data](https://www.ncbi.nlm.nih.gov/pubmed/25348409)
-- Human Phenotype Ontology (hp): [The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease.](https://www.ncbi.nlm.nih.gov/pubmed/18950739)
-- Human developmental anatomy, abstract (ehdaa2): [A new ontology (structured hierarchy) of human developmental anatomy for the first 7 weeks (Carnegie stages 1-20).](https://www.ncbi.nlm.nih.gov/pubmed/22973865)
-- Hymenoptera Anatomy Ontology (hao): [A gross anatomy ontology for hymenoptera](https://www.ncbi.nlm.nih.gov/pubmed/21209921)
-- Interaction Network Ontology (ino): [Development and application of an Interaction Network Ontology for literature mining of vaccine-associated gene-gene interactions](https://doi.org/10.1186/2041-1480-6-2)
-- Kinetic Simulation Algorithm Ontology (kisao): [Controlled vocabularies and semantics in systems biology](https://www.ncbi.nlm.nih.gov/pubmed/22027554)
-- MIAPA Ontology (miapa): [Taking the First Steps towards a Standard for Reporting on Phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA)](https://doi.org/10.1089/omi.2006.10.231)
-- Mammalian Phenotype Ontology (mp): [The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data](https://www.ncbi.nlm.nih.gov/pubmed/22961259)
-- Mass spectrometry ontology (ms): [The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.](https://www.ncbi.nlm.nih.gov/pubmed/23482073)
-- Measurement method ontology (mmo): [Three ontologies to define phenotype measurement data.](https://www.ncbi.nlm.nih.gov/pubmed/22654893)
-- Mondo Disease Ontology (mondo): [Mondo: Unifying diseases for the world, by the world](https://www.medrxiv.org/content/10.1101/2022.04.13.22273750)
-- Neuro Behavior Ontology (nbo): [Analyzing gene expression data in mice with the Neuro Behavior Ontology](https://www.ncbi.nlm.nih.gov/pubmed/24177753)
-- Ontology for Biomedical Investigations (obi): [The Ontology for Biomedical Investigations](https://www.ncbi.nlm.nih.gov/pubmed/27128319)
-- Ontology for Nutritional Studies (ons): [ONS: an ontology for a standardized description of interventions and observational studies in nutrition](https://www.ncbi.nlm.nih.gov/pubmed/29736190)
-- Ontology of Host Pathogen Interactions (ohpi): [Victors: a web-based knowledge base of virulence factors in human and animal pathogens](https://www.ncbi.nlm.nih.gov/pubmed/30365026)
-- Ontology of Medically Related Social Entities (omrse): [The ontology of medically related social entities: recent developments](https://www.ncbi.nlm.nih.gov/pubmed/27406187)
-- Ontology of Microbial Phenotypes (omp): [An ontology for microbial phenotypes](https://doi.org/10.1186/s12866-014-0294-3)
-- Oral Health and Disease Ontology (ohd): [Structuring, reuse and analysis of electronic dental data using the Oral Health and Disease Ontology](https://www.ncbi.nlm.nih.gov/pubmed/32819435)
-- PRotein Ontology (PRO) (pr): [Protein Ontology (PRO): enhancing and scaling up the representation of protein entities](https://www.ncbi.nlm.nih.gov/pubmed/27899649)
-- Pathogen Host Interaction Phenotype Ontology (phipo): [PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions](https://www.ncbi.nlm.nih.gov/pubmed/34788826)
-- Pathogen Transmission Ontology (trans): [GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database](https://www.ncbi.nlm.nih.gov/pubmed/19850722)
-- Pathway ontology (pw): [The Rat Genome Database pathway portal.](https://www.ncbi.nlm.nih.gov/pubmed/21478484)
-- Phenotype And Trait Ontology (pato): [The anatomy of phenotype ontologies: principles, properties and applications](https://www.ncbi.nlm.nih.gov/pubmed/28387809)
-- Plant Environment Ontology (eo): [Ontologies as integrative tools for plant science.](https://www.ncbi.nlm.nih.gov/pubmed/22847540)
-- Plant Experimental Conditions Ontology (peco): [The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.](https://www.ncbi.nlm.nih.gov/pubmed/29186578)
-- Plant Ontology (po): [The plant ontology as a tool for comparative plant anatomy and genomic analyses.](https://www.ncbi.nlm.nih.gov/pubmed/23220694)
-- Plant Stress Ontology (pso): [The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.](https://www.ncbi.nlm.nih.gov/pubmed/29186578)
-- Plant Trait Ontology (to): [The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.](https://www.ncbi.nlm.nih.gov/pubmed/29186578)
-- Porifera Ontology (poro): [The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology](https://www.ncbi.nlm.nih.gov/pubmed/25276334)
-- Protein modification (mod): [The PSI-MOD community standard for representation of protein modification data](https://www.ncbi.nlm.nih.gov/pubmed/18688235)
-- Rat Strain Ontology (rs): [Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD.](https://www.ncbi.nlm.nih.gov/pubmed/24267899)
-- Sequence types and features ontology (so): [The Sequence Ontology: a tool for the unification of genome annotations.](https://www.ncbi.nlm.nih.gov/pubmed/15892872)
-- Sickle Cell Disease Ontology (scdo): [The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation.](https://www.ncbi.nlm.nih.gov/pubmed/35363306)
-- Software ontology (swo): [The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation](https://www.ncbi.nlm.nih.gov/pubmed/25068035)
-- Spider Ontology (spd): [The Spider Anatomy Ontology (SPD)—A Versatile Tool to Link Anatomy with Cross-Disciplinary Data](https://doi.org/10.3390/d11100202)
-- Symptom Ontology (symp): [GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database](https://www.ncbi.nlm.nih.gov/pubmed/19850722)
-- Taxonomic rank vocabulary (taxrank): [The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes](https://doi.org/10.1186/2041-1480-4-34)
-- Teleost Anatomy Ontology (tao): [The teleost anatomy ontology: anatomical representation for the genomics age](https://www.ncbi.nlm.nih.gov/pubmed/20547776)
-- Teleost taxonomy ontology (tto): [The Teleost Taxonomy Ontology](https://doi.org/10.1038/npre.2010.4629.1)
-- The Drug Ontology (dron): [Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request](https://doi.org/10.1186/s13326-017-0121-5)
-- The Drug-Drug Interactions Ontology (dinto): [DINTO: Using OWL Ontologies and SWRL Rules to Infer Drug–Drug Interactions and Their Mechanisms.](https://www.ncbi.nlm.nih.gov/pubmed/26147071)
-- The Prescription of Drugs Ontology (pdro): [The Prescription of Drug Ontology 2.0 (PDRO): More Than the Sum of Its Parts](https://www.ncbi.nlm.nih.gov/pubmed/34831777)
-- Toxic Process Ontology (txpo): [Ontological approach to the knowledge systematization of a toxic process and toxic course representation framework for early drug risk management](https://www.ncbi.nlm.nih.gov/pubmed/32883995)
-- Uberon multi-species anatomy ontology (uberon): [Uberon, an integrative multi-species anatomy ontology](https://www.ncbi.nlm.nih.gov/pubmed/22293552)
-- Unified phenotype ontology (uPheno) (upheno): [Phenotype Ontologies Traversing All The Organisms (POTATO) workshop aims to reconcile logical definitions across species](https://zenodo.org/record/2382757)
-- Unipathway (upa): [UniPathway: a resource for the exploration and annotation of metabolic pathways](https://www.ncbi.nlm.nih.gov/pubmed/22102589)
-- Units of measurement ontology (uo): [The Units Ontology: a tool for integrating units of measurement in science](https://www.ncbi.nlm.nih.gov/pubmed/23060432)
-- VEuPathDB ontology (eupath): [Malaria study data integration and information retrieval based on OBO Foundry ontologies.](https://doi.org/10.5281/zenodo.6685957)
-- Vaccine Ontology (vo): [Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses](https://www.ncbi.nlm.nih.gov/pubmed/23256535)
-- Vertebrate Taxonomy Ontology (vto): [The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes](https://doi.org/10.1186/2041-1480-4-34)
-- Xenopus Anatomy Ontology (xao): [An ontology for Xenopus anatomy and development.](https://www.ncbi.nlm.nih.gov/pubmed/18817563)
-- Xenopus Phenotype Ontology (xpo): [The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development.](https://www.ncbi.nlm.nih.gov/pubmed/35317743)
-- Zebrafish anatomy and development ontology (zfa): [The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio.](https://www.ncbi.nlm.nih.gov/pubmed/24568621)
-- clinical LABoratory Ontology (labo): [LABO: An Ontology for Laboratory Test Prescription and Reporting](https://doi.org/10.5281/zenodo.6522019)
-- planaria-ontology (plana): [Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms](https://www.ncbi.nlm.nih.gov/pubmed/34318308)
+<ul>
+{% for ontology in site.ontologies %}
+{% for publication in ontology.publications %}
+<li>
+    {{ ontology.title }} ({{ ontology.id }}):
+    <a href="{{ publication.id }}">{{ publication.title }}</a>
+</li>
+{% endfor %}
+{% endfor %}
+</ul>