HPO release info, April 2019


Dear HPO Users.

The HPO consortium is announcing the April 2019 release of HPO and its associated resources.

First and foremost we would like to announce that we are now using the Ontology Development Toolkit (ODK) for quality control and releases. This was mainly driven by Nico Matenzoglu (see https://github.com/INCATools/ontology-development-kit). There may be a few minor changes in the generated files. Please report any serious (probably unintended) changes to us.
With the switch to ODK, it is now possible to start using DOSDP (https://github.com/INCATools/dead_simple_owl_design_patterns), which we are beginning to do in a coordinated manner together with other phenotype ontologies (e.g. mouse, zebrafish). These efforts are driven by David Osumi-Sutherland, Nico, Leigh, and Nicole (see https://github.com/obophenotype/upheno/wiki/Phenotype-Ontologies-Reconciliation-Effort).
We have cleaned up the import section of HPO. The imports are used for linking HPO to external building-block ontologies such as Uberon, GO, or ChEBI. We have added more medical abbreviations that are commonly used. Finally, we have fixed several typos and bugs in labels and textual definitions.

The set of files in the release of HPO will be extended throughout the next months. As a first step, we have added the JSON serialisation (https://github.com/geneontology/obographs/). This will probably be more convenient for users of several programming languages and will hopefully remove the need for yet another OBO parser. Two more release files of importance are the hp-base and the experimental hp-full version of the ontology. These are recommended by the OBO foundry for the following purposes. hp-base is an ontology that only contains HP-native axioms and no axiom that belongs to any of the ontologies that HP depends on, such as GO or CHEBI. This ontology is mainly important for ontology editors wishing to import HP alone without its imports. hp-full is an experimental version of the ontology that contains, in addition to the normal release, the *unreviewed* inferred axioms. This ontology should only be used for the special cases it was intended for. More information about these release products can be found here (https://github.com/INCATools/ontology-development-kit/issues/194).
It is also important to note, that HPO now does contain a slightly different format for the version number. The format “releases/<date>”, has been replaced by “hp/releases/<date>”. The annotation in hp.obo that previously was “ontology: hp” has now been changed to “ontology: hp.obo”.

The HPO disease models have also been updated extensively. Besides manual curation and synchronisation with OMIM, we have added the inheritance mode for over 300 entries that previously did not have any information about the inheritance.

Last, but not least, we have changed the way you, our users, can inform us about bugs and missing terms in HPO. Upon selecting “New issue”, you will now have the opportunity to select one out of seven different “ticket-types” (see https://github.com/obophenotype/human-phenotype-ontology/issues/new/choose).

We hope the above described changes are useful to our users. Should you need any further information, please do not hesitate to contact us or file an issue on our tracker.

The HPO Team

Prof. Dr. Sebastian Köhler
Berlin Institute of Health | Charité | Einstein Center Digital Future
www.bihealth.org | www.digital-future.berlin | drseb.github.io | phenomics.github.io

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