Merge pull request #120 from monarch-initiative/doc-update

Update composition docs to match ODK config

Author: caufieldjh

docs/composition.md

@@ -1,43 +1,133 @@
 # Composition of PHENIO
 
-* **BFO**: Basic Formal Ontology (https://basic-formal-ontology.org/) - an ontology that provides a set of upper-level categories for organizing knowledge and facilitating interoperability between other ontologies and domain-specific applications.
+PHENIO (Phenomics Integrated Ontology) is an application ontology that integrates multiple ontologies and data sources to enable cross-species phenotype comparisons. This page documents all ontologies, components, and mapping sets included in PHENIO.
 
-* **CARO**: Common Anatomy Reference Ontology (https://www.obofoundry.org/ontology/caro.html) - an ontology that standardizes the annotation and representation of anatomical structures across different species.
+For details on the difference between PHENIO and uPHENO, see [PHENIO vs uPHENO](phenio_vs_upheno.md).
 
-* **CHEBI**: Chemical Entities of Biological Interest (https://www.ebi.ac.uk/chebi/) -  a dictionary of molecular entities.
+## Import Modules
+
+Import modules are ontologies included via the OBO standard import mechanism. PHENIO uses base-merging to include only the terms directly asserted in each source ontology.
+
+### Upper-Level and Foundational Ontologies
+
+* **BFO**: Basic Formal Ontology (https://basic-formal-ontology.org/) - an upper-level ontology that provides a set of categories for organizing knowledge and facilitating interoperability between ontologies.
+
+* **RO**: Relations Ontology (http://www.obofoundry.org/ontology/ro.html) - an ontology that defines relationships between entities in other ontologies, providing a foundation for relating information across different domains.
+
+* **PATO**: Phenotypic Quality Ontology (http://www.obofoundry.org/ontology/pato.html) - an ontology that provides a standardized vocabulary to describe phenotypic qualities, such as height, weight, and shape.
 
 * **ECO**: Evidence and Conclusion Ontology (https://evidenceontology.org/) - an ontology that categorizes and organizes different types of evidence used in scientific research and draws conclusions based on that evidence.
 
-* **EMAPA**: Mouse Developmental Anatomy Ontology (https://obofoundry.org/ontology/emapa.html)- an ontology that provides a standardized framework for describing spatial and temporal gene expression patterns during mouse development.
+### Chemical and Molecular Ontologies
 
-* **FAO**: Fungal Anatomy Ontology (https://obofoundry.org/ontology/fao.html) - a structured controlled vocabulary for the anatomy of fungi.
+* **CHEBI (Slim)**: Chemical Entities of Biological Interest (https://www.ebi.ac.uk/chebi/) - a dictionary of molecular entities; PHENIO uses a simplified subset (available from https://github.com/obophenotype/chebi_obo_slim).
 
-* **FBBT**: FlyBase Drosophila Gross Anatomy Ontology (https://obofoundry.org/ontology/fbbt) - an ontology that describes the gross anatomy of the fruit fly Drosophila melanogaster.
+* **PR (Slim)**: Protein Ontology (https://obofoundry.org/ontology/pr.html) - an ontology of protein types covering organisms of biomedical interest; PHENIO uses a simplified subset (available from https://github.com/obophenotype/pro_obo_slim).
 
-* **GO**: Gene Ontology (http://geneontology.org/) - a widely-used ontology that categorizes gene products' functions in various biological processes, cellular components, and molecular functions.
+### Gene and Sequence Identifiers
 
-* **HSAPDV**: Human Developmental Stage Ontology (https://obofoundry.org/ontology/hsapdv) - an ontology of human developmental stages, covering both embryonic (Carnegie) stages and adult stages.
+* **NCBI Gene**: NCBI Gene (https://www.ncbi.nlm.nih.gov/gene) - NCBI Gene identifiers for cross-referencing genes across species.
 
-* **MONDO**: Monarch Disease Ontology (https://mondo.monarchinitiative.org/) - an ontology that integrates disease-related information from various sources to facilitate the understanding of human diseases.
+* **HGNC**: HUGO Gene Nomenclature Committee (https://www.genenames.org/) - standardized gene naming and identifiers for human genes.
+
+* **SO**: Sequence Ontology (https://obofoundry.org/ontology/so.html) - an ontology describing biological sequence features, attributes, and relationships.
+
+* **Monochrom**: Chromosome Ontology (https://github.com/monarch-initiative/monochrom) - an ontology of chromosomes for representing karyotype information.
+
+### Spatial Ontology
+
+* **BSPO**: Biological Spatial Ontology (https://obofoundry.org/ontology/bspo.html) - an ontology for representing spatial and positional relationships of anatomical entities.
+
+### Developmental Stage Ontologies
+
+* **WBls**: WormBase Life Stages (https://obofoundry.org/ontology/wbls.html) - an ontology of life stages for *C. elegans*.
+
+* **ZFS**: Zebrafish Stages (https://obofoundry.org/ontology/zfs.html) - an ontology of zebrafish developmental stages.
+
+* **FBdv**: FlyBase Development Ontology (https://obofoundry.org/ontology/fbdv.html) - an ontology of *Drosophila melanogaster* developmental stages.
+
+### Pathology and Behavior Ontologies
+
+* **MPATH**: Mouse Pathology Ontology (https://obofoundry.org/ontology/mpath.html) - an ontology that standardizes and classifies phenotypic abnormalities observed in various mutant mouse strains.
+
+* **NBO**: Neuro Behavior Ontology (https://obofoundry.org/ontology/nbo.html) - an ontology that defines behavioral and neurological phenotypes to support research in neuroscience and behavior genetics.
+
+### Taxonomy
+
+* **NCBITaxon (Slim)**: NCBI Taxonomy (https://www.ncbi.nlm.nih.gov/taxonomy) - a taxonomy database that classifies and names living organisms; PHENIO uses a simplified subset (available from http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl).
+
+## Components
+
+Components are ontologies merged into PHENIO as full modules using their base release, rather than being subset by PHENIO-specific terms.
+
+### Phenotype Ontologies
+
+* **uPHENO**: Unified Phenotype Ontology (https://github.com/obophenotype/upheno) - a framework ontology that links phenotypic abnormalities to the anatomical entities that are affected, enabling cross-species genotype-phenotype comparisons.
+
+* **HP**: Human Phenotype Ontology (https://hpo.jax.org/) - a standardized vocabulary of phenotypic abnormalities observed in human disease.
 
-* **MPATH**: Mouse Pathology Ontology (http://www.pathbase.net/Pathology_Ontology/index.php) - an ontology that standardizes and classifies phenotypic abnormalities observed in various mutant mouse strains.
+* **MP**: Mammalian Phenotype Ontology (https://obofoundry.org/ontology/mp.html) - an ontology of phenotypic abnormalities observed in mammals, primarily mouse.
 
-* **NBO**: Neuro Behavior Ontology (http://www.obofoundry.org/ontology/nbo.html) - an ontology that defines behavioral and neurological phenotypes to support research in neuroscience and behavior genetics.
+* **ZP**: Zebrafish Phenotype Ontology (https://obofoundry.org/ontology/zp.html) - an ontology of phenotypes observed in zebrafish (*Danio rerio*).
 
-* **NCBITaxon (Slim)**: NCBI Taxonomy (https://www.ncbi.nlm.nih.gov/taxonomy) - a taxonomy database that classifies and names living organisms; this is a simplified subset (available from http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl).
+* **XPO**: Xenopus Phenotype Ontology (https://obofoundry.org/ontology/xpo.html) - an ontology of phenotypes observed in *Xenopus* (frogs).
+
+* **DPO**: Drosophila Phenotype Ontology (https://obofoundry.org/ontology/dpo.html) - an ontology of phenotypes observed in *Drosophila melanogaster*.
+
+* **FYPO**: Fission Yeast Phenotype Ontology (https://obofoundry.org/ontology/fypo.html) - an ontology of phenotypes observed in fission yeast (*Schizosaccharomyces pombe*).
+
+* **WBPhenotype**: WormBase Phenotype Ontology (https://obofoundry.org/ontology/wbphenotype.html) - an ontology of phenotypes observed in *Caenorhabditis elegans*.
+
+* **DDPHENO**: Dictyostelium Phenotype Ontology (https://obofoundry.org/ontology/ddpheno.html) - an ontology of phenotypes observed in *Dictyostelium discoideum* (slime mold).
 
 * **OBA**: Ontology of Biological Attributes (https://obofoundry.org/ontology/oba.html) - an ontology that describes biological attributes such as size, shape, color, and behavior across different species.
 
-* **PATO**: Phenotypic Quality Ontology (http://www.obofoundry.org/ontology/pato.html) - an ontology that provides a standardized vocabulary to describe phenotypic qualities, such as height, weight, and shape.
+### Disease and Medical Action Ontologies
+
+* **MONDO**: Monarch Disease Ontology (https://mondo.monarchinitiative.org/) - an ontology that integrates disease-related information from various sources to facilitate the understanding of human diseases.
+
+* **MAXO**: Medical Action Ontology (https://obofoundry.org/ontology/maxo.html) - an ontology of medical procedures, interventions, and therapies used in the treatment of diseases.
+
+### Gene Ontology
+
+* **GO**: Gene Ontology (http://geneontology.org/) - a widely-used ontology that categorizes gene products' functions in various biological processes, cellular components, and molecular functions.
+
+### Anatomy Ontologies
+
+* **UBERON**: Integrated Cross-Species Anatomy Ontology (https://obofoundry.org/ontology/uberon.html) - an ontology that integrates anatomical information from different species, facilitating cross-species comparisons.
+
+* **CL**: Cell Ontology (https://obofoundry.org/ontology/cl.html) - an ontology representing cell types across species.
+
+* **ZFA**: Zebrafish Anatomy and Development Ontology (https://obofoundry.org/ontology/zfa.html) - an ontology that describes the anatomy and developmental stages of the zebrafish (*Danio rerio*).
+
+* **XAO**: Xenopus Anatomy Ontology (https://obofoundry.org/ontology/xao.html) - an ontology of the anatomical structures of *Xenopus*.
+
+* **FBBT**: FlyBase Drosophila Gross Anatomy Ontology (https://obofoundry.org/ontology/fbbt.html) - an ontology that describes the gross anatomy of *Drosophila melanogaster*.
+
+* **WBBT**: WormBase Gross Anatomy Ontology (https://obofoundry.org/ontology/wbbt.html) - an ontology that describes the gross anatomy of *Caenorhabditis elegans*.
+
+* **DDANAT**: Dictyostelium Anatomy Ontology (https://obofoundry.org/ontology/ddanat.html) - an ontology of anatomical structures in *Dictyostelium discoideum*.
+
+* **EMAPA**: Mouse Developmental Anatomy Ontology (https://obofoundry.org/ontology/emapa.html) - an ontology that provides a standardized framework for describing spatial and temporal gene expression patterns during mouse development.
+
+### Life Stage Ontologies
+
+* **HsapDv**: Human Developmental Stage Ontology (https://obofoundry.org/ontology/hsapdv.html) - an ontology of human developmental stages, covering both embryonic (Carnegie) stages and adult stages.
+
+## Bridge and Alignment Modules
+
+Bridge ontologies provide the axioms that link species-specific ontologies to their cross-species counterparts, enabling cross-species inference.
+
+* **uPHENO Bridge**: (https://github.com/obophenotype/upheno) - bridge axioms linking species-specific phenotype ontologies to uPHENO.
 
-* **RO**: Relations Ontology (http://www.obofoundry.org/ontology/ro.html) - an ontology that defines relationships between entities in other ontologies and provides a foundation for relating information across different domains.
+* **uPHENO Alignments**: (https://github.com/obophenotype/upheno) - alignment axioms for phenotype ontology integration across species.
 
-* **STATO**: Statistical Methods Ontology (https://stato-ontology.org/) - an ontology that represents statistical methods and concepts used in the analysis of biological and clinical data.
+## SSSOM Mapping Sets
 
-* **UBERON**: Integrated Cross-Species Anatomy Ontology (http://www.obofoundry.org/ontology/uberon.html) - an ontology that integrates anatomical information from different species, facilitating cross-species comparisons.
+PHENIO includes [Simple Standard for Sharing Ontological Mappings (SSSOM)](https://mapping-commons.github.io/sssom/) mapping sets that define equivalences and relationships between terms in different ontologies.
 
-* **UPHENO**: Uberon Phenotype Ontology (https://github.com/obophenotype/upheno) - an ontology that links phenotypic abnormalities to the anatomical entities that are affected, enabling the study of genotype-phenotype relationships.
+* **Uberon SSSOM Mappings**: (http://purl.obolibrary.org/obo/uberon/uberon.sssom.tsv) - cross-species anatomy mappings.
 
-* **WBBT**: WormBase Gross Anatomy Ontology (http://www.obofoundry.org/ontology/wbphenotype.html) - an ontology that describes the gross anatomy of the nematode worm Caenorhabditis elegans.
+* **CL SSSOM Mappings**: (http://purl.obolibrary.org/obo/cl/cl.sssom.tsv) - cell type mappings.
 
-* **ZFA**: Zebrafish Anatomy and Development Ontology (http://www.obofoundry.org/ontology/zfa.html) - an ontology that describes the anatomy and developmental stages of the zebrafish (Danio rerio).
+* **uPHENO-OBA SSSOM Mappings**: (https://github.com/obophenotype/upheno) - mappings between uPHENO and OBA.