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Add doc/example for ICPHT #61

Open mellybelly opened 8 years ago

mellybelly commented 8 years ago

In the paper we suggest that use of the International Consortium of Human Phenotype Terminologies is a suitable alternative to HPO. We should add an example and documentation supporting this.

http://www.irdirc.org/ichpt/

pnrobinson commented 8 years ago

I would suggest that we either say that one can use one of a number of clinical terminologies (POSSUM, London, phenodb, ICHPT, HPO, SNOMED, etc) or that we recommend HPO. ICHPT is not really supported by anyone (i.e., it has exactly zero funding right now), and with the UMLS mapping there is less of a need for it now anyway. Also, if we want people to use the phenopacket for non genetic disease, then we should be realistic and allow SNOMED. We need to try to work with SNOMED to get allowed and fully open mappings! -Peter

Professor of Medical Genomics Professor of Bioinformatics, Freie Universität Berlin Institut für Medizinische Genetik und Humangenetik Charité - Universitätsmedizin Berlin Augustenburger Platz 1 13353 Berlin Germany +4930 450566006 Mobile: 0160 93769872 peter.robinson@charite.de http://compbio.charite.de http://www.human-phenotype-ontology.org I have learned from my mistakes, and I am sure I can repeat them exactly ORCID ID:http://orcid.org/0000-0002-0736-9199 Scopus Author ID 7403719646 Appointment request: http://doodle.com/pnrobinson

Von: Melissa Haendel [notifications@github.com] Gesendet: Dienstag, 5. April 2016 15:55 An: phenopackets/phenopacket-format Betreff: [phenopackets/phenopacket-format] Add doc/example for ICPHT (#61)

In the paper we suggest that use of the International Consortium of Human Phenotype Terminologies is a suitable alternative to HPO. We should add an example and documentation supporting this.

http://www.irdirc.org/ichpt/

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHubhttps://github.com/phenopackets/phenopacket-format/issues/61

cmungall commented 8 years ago

Currently the format itself is unrestricted, any ontology class ID can go in the various slots (which is necessary and pxf can be used for yeast or zebrafish too).

We can provide recommendations, either informative or normative (the latter would be of the form "for human patients, the phenotype ID MUST be drawn from X, Y or Z).

We could also have a wider variety of examples, more examples definitely helpful.

We have one example with SNOMED (where SNOMED is used for the exposure - smoking)