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<img src="https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/upheno-logos/upheno-logo_black-banner.svg?sanitize=true" width="400px"/>

This repository contains common files ontologies and workflows shared
between multiple phenotype ontologies.
The persistent URL (PURL) for uPheno is: `http://purl.obolibrary.org/obo/upheno.owl`.

See the [wiki](https://github.com/obophenotype/upheno/wiki) for additional documentation
Quick links:

## Inter-ontology Closest Matches
- [Documentation](https://obophenotype.github.io/upheno/)
- [Core concepts on Phenotype Data](https://obophenotype.github.io/upheno/reference/core-concepts/)
- [Phenotype reconciliation effort](https://obophenotype.github.io/upheno/reference/reconciliation-effort/)
- [Phenotype data in practice](https://obophenotype.github.io/upheno/reference/phenotype-data/)
- [Integrating phenotype data with the uPheno framework](https://obophenotype.github.io/upheno/reference/data-integration/)
- [Report (under submission in Genetics)](https://www.biorxiv.org/content/10.1101/2024.09.18.613276v1)
- [uPheno mappings (in Monarch mapping commons)](https://data.monarchinitiative.org/mappings/latest/index.html)
- [Browse uPheno on OLS](https://www.ebi.ac.uk/ols4/ontologies/upheno)
- [Check out uPheno phenotypes in the Monarch App (example: glucose level in blood)](https://monarchinitiative.org/UPHENO:0051766)
- [uPheno Ontology releases](https://github.com/obophenotype/upheno-dev/)

* [hp-to-mp-bestmatches.tsv](mappings/hp-to-mp-bestmatches.tsv)
* [hp-to-zp-bestmatches.tsv](mappings/hp-to-zp-bestmatches.tsv)
* [hp-to-wbphenotype-bestmatches.tsv](mappings/hp-to-wbphenotype-bestmatches.tsv)

See [mappings/README.md](mappings/README.md) for explanation of fields

## Background

Many databases use their own ontology geared towards their species of
interest or an area of interest. The purpose of this repository is to
provide a mechanism for integrating these together into a unified
phenotype ontology. We do this primarily through *OWL Axiomatization*
and *OWL Reasoning*.

This approach takes advantages of the fact that phenotype ontologies
typically follow a compositional structure. If each contributing
ontology makes the semantics of this composition transparent through
*OWL Axioms* then a reasoner can piece the ontologies together and
find the overarching classification.

For example, if a phenotype ontology `A` contains a class for `limb size`,
and also provides an OWL axiom that maps onto a decomposed form, for
example:

* `A:limb size` equivalentTo `pato:size` and `inheres in` some `limb`

And if phenotype ontology `B` has a class `short forelimb`, with axiom:

* `B:short forelimb` equivalentTo `pato:short` and `inheres in` some `forelimb`

Then a reasoner can infer that `B:short forelimb` is a subclass of `A:limb size`

The OWL Axioms we use follow a design pattern called `EQ` or `Entity-Quality` descriptions.

Furthermore, if a database `C` provides a row for a genotype described
compositionally, the placement of these phenotypes can also be
inferred.

For background on the original formulation, see:

C J Mungall, Georgios Gkoutos, Cynthia Smith, Melissa Haendel, Suzanna Lewis, Michael Ashburner (2010) [Integrating phenotype ontologies across multiple species](http://genomebiology.com/2010/11/1/R2) _Genome Biology_ 11 (1)

## Exploring uPheno

The Monarch website uses uPheno to group data from multiple species. See for example: https://monarchinitiative.org/phenotype/MP:0003631

You can also query this using Monarch SciGraph services: https://scigraph-ontology.monarchinitiative.org/scigraph/docs/

To understand the mechanics of how uPheno works, we recommend opening
the OWL in Protege and exploring with a fast reasoner such as Elk
running

The remainder of these docs assumes some familiarity with Protege/OWL

We provide various modules:

* mammal.owl
* vertebrate.owl
* metazoa.owl

## Contributing Ontologies

* [mp](http://obofoundry.org/ontology/mp.html)* - mouse // mammal.owl
* [hp](http://obofoundry.org/ontology/hp.html)* - human // mammal.owl
* zp - zebrafish** // vertebrate.owl
* [wbphenotype](http://obofoundry.org/ontology/wbphenotype.html) - C elegans // metazoa.owl
* [dpo](http://obofoundry.org/ontology/dpo.html)* - Drosophila // metazoa.owl
* [fypo](http://obofoundry.org/ontology/fypo.html)* - Fission Yeast // eukaryote.owl

`*` -- this ontology provides their own OWL axiomatization
`**` -- separately generated ontology

## External Imports Modules

The OWL axiomatization depends on a number of external ontologies, including

* pato
* uberon
* cl
* species-specific AOs
* go
* chebi

Many of these are large, so we create *import modules* in the upheno ontology purl space

See the [imports](imports) directory

## PURLs

This ontology has the OBO PURL `upheno`

A redirect at [obolibrary.org](https://github.com/OBOFoundry/purl.obolibrary.org/) maps

* http://purl.obolibrary.org/obo/upheno/ ==> this repository on github

## History

Previously we had various things on:

* https://code.google.com/p/phenotype-ontologies

This was split across multiple github repos

* {data,server} ==> https://github.com/monarch-initiative/monarch-owlsim-data
* src/ontology
* mp ==> https://github.com/obophenotype/mammalian-phenotype-ontology/
* hp ==> https://github.com/obophenotype/human-phenotype-ontology/ (may change)
* imports/ ==> https://github.com/obophenotype/upheno
* monarch.owl ==> https://github.com/monarch-initiative/monarch-ontology
* zp.owl ==> http://compbio.charite.de/jenkins/job/zp-owl/
* wiki ==> https://github.com/obophenotype/upheno ([docs/](docs/) directory)

## Design patterns

The design patterns are grouped into three higher level groupings:
1. anatomical entity (anatomical entities (Uberon), cells (CL))
2. cellular component (from GO)
3. chemical entity (includes chemicals (CHEBI), proteins (PRO))

Current structure of uPheno 1:


1. mp-hp-kboom.owl: OBSOLETE
1. mp-hp.ow: OBSOLETE
1. upheno_root_alignments.owl: OBSOLETE

## Current uPheno structure
1. upheno.owl (TODO needs to be obsoleted):
1. metazoa.owl
1. Worm
1. OBO:uberon/bridge/cl-bridge-to-wbbt.owl
1. OBO:uberon/bridge/uberon-bridge-to-wbbt.owl
1. OBO:wbphenotype/wbphenotype-full.owl
1. Fly
1. OBO:uberon/bridge/cl-bridge-to-fbbt.owl
1. OBO:uberon/bridge/uberon-bridge-to-fbbt.owl
1. OBO:dpo.owl
1. OBO:upheno/dpo/dpo-bridge.owl
1. OBO:upheno/imports/fbbt_phenotype.owl
1. OBO:upheno/vertebrate.owl
1. Zebrafish:
1. OBO:zp.owl
1. OBO:uberon/bridge/cl-bridge-to-zfa.owl
1. OBO:uberon/bridge/uberon-bridge-to-zfa.owl
1. OBO:upheno/imports/zfa_import.owl
1. OBO:vt.owl (<- this currently points to uPheno, made [ticket](https://github.com/AnimalGenome/vertebrate-trait-ontology/issues/3) to change that)
1. upheno internal:
1. OBO:upheno/imports/uberon_import.owl
1. OBO:upheno/mammal.owl
1. OBO:mp.owl
1. OBO:hp.owl
1. upheno internal:
1. OBO:upheno/hp-mp/mp_hp-align-equiv.owl (REMOVED)
1. OBO:upheno/upheno_root_alignments.owl (covered, root terms under uPheno:"Phenotype")
1. OBO:upheno/imports/go_phenotype.owl (TODO)
1. OBO:upheno/imports/mpath_phenotype.owl (TODO)
1. OBO:upheno/imports/nbo_phenotype.owl (TODO)
1. OBO:upheno/imports/uberon_phenotype.owl (TODO)

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