"Mild", "Moderate" "Severe" - potential for HPO terms

[obophenotype-user]

Hi All,

As has been raised at least once in the past, there is some inconsistency in the availability of the modifiers "mild", "moderate", "severe". Recently a user was wondering if these concepts would be appropriate for addition to the ontology on their own, so that users would be able to use an official HPO term as a modifier of another. We would certainly appreciate your thoughts on this matter.

Sincerely, Heather Trang

PhenoTips team member

Reported by: heathertrang

Original Ticket: obo/human-phenotype-requests/298

[obophenotype-user]

• status: unread --> pending
• assigned_to: Peter N. Robinson

Original comment by: pnrobinson

[obophenotype-user]

This is a good idea, and we will be basically mapping these terms to PATO and then making sure there is a good way of keeping track of everything. More to follow. -Peter

Original comment by: pnrobinson

[obophenotype-user]

Hi everybody, I have had a look at PATO and thought a little bit about how to create a hierarchy of modifiers. I think we need something like this

modifier --intensity --duration --occurence --position --spatial pattern --not sure how to include SECONDARY (?observed causality) --response-to-treatment

For many of these, there is a basis in PATO. However, we will need to write our own definitions and probably say that the terms are children of the PATO terms. We will need to add quite a few terms to PATO. Here is what I found:

intensity PATO:0000049 --mild --moderate --severe (additionally need: borderline, profound)

duration quality of a process PATO:0001309 --acute --subacute --chronic (Not sure what to do about PATO term "duration of disease")

occurrence quality PATO:0000057 (Note: this is not consistent, either remove "of a process" from "duration quality" or add it here) --non-progressive --progressive --recurrent (Note the PATO term sporadic is used in the sense of "recurrent" in scattered intervals, but I do not think this word is optimal, in medicine sporadic means "occuring once out of the blue", e.g. a sporadic mutation) (Missing: episodic)

position --distal to (this is a relative adjective, but I think we want the absolute adjective "distal" which I did not find in PATO) --proximal to (ditto) --bilateral (Unilateral is missing)

spatial pattern --generalized --localised (this is inconsistent, mix of UK and US spellings)

Missing --refractory --secondary

Original comment by: pnrobinson

[obophenotype-user]

• status: pending --> closed-accepted

Original comment by: pnrobinson

[obophenotype-user]

Hi Heather and everybody, I have now developed the new "Clinical modifer" subontology, which addresses Heather's comment. I have tried to put all of the items that we are using as Annotation modifers into this subontology, which should clean things up a bit. Comments, please!

Original comment by: pnrobinson

[obophenotype-user]

Peter, I addressed these in PATO, were you able to take a look? (in the edit file) I would really like this vocabulary to be available for all the phenotype ontologies. We can reconcile at hackathon.

Original comment by: mellybelly

[obophenotype-user]

Hi Melissa, I think that the use of these modifiers in human medicine is specification of the PATO definitions, but I thought we had decided to basically define them using equivalencies in the OWL version of the HPO. I do not think it is a good idea to use the PATO definitions directly in software like phenotips, and I still think there are lots of issues with PATO. We should try to go through a lot of the sections that are relevant to human disease, I am often not sure why certain terms are there or why certain choices were made for the structure. -Peter

Dr. med. Peter N. Robinson, MSc. Professor of Medical Genomics Professor in the Bioinformatics Division of the Department of Mathematics and Computer Science of the 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 Introduction to Bio-Ontologies: http://www.crcpress.com/product/isbn/9781439836651 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

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Von: Melissa Haendel [mellybelly@users.sf.net] Gesendet: Freitag, 6. Juni 2014 15:26 An: [obo:human-phenotype-requests] Betreff: [obo:human-phenotype-requests] #298 "Mild", "Moderate" "Severe" - potential for HPO terms

Peter, I addressed these in PATO, were you able to take a look? (in the edit file) I would really like this vocabulary to be available for all the phenotype ontologies. We can reconcile at hackathon.

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[human-phenotype-requests:#298]http://sourceforge.net/p/obo/human-phenotype-requests/298/ "Mild", "Moderate" "Severe" - potential for HPO terms

Status: closed-accepted Group: musculoskeletal Created: Sat Apr 19, 2014 02:51 PM UTC by Heather Trang Last Updated: Fri Jun 06, 2014 05:52 AM UTC Owner: Peter N. Robinson

Hi All,

As has been raised at least once in the past, there is some inconsistency in the availability of the modifiers "mild", "moderate", "severe". Recently a user was wondering if these concepts would be appropriate for addition to the ontology on their own, so that users would be able to use an official HPO term as a modifier of another. We would certainly appreciate your thoughts on this matter.

Sincerely, Heather Trang

PhenoTips team member

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Original comment by: pnrobinson

[obophenotype-user]

I agree that the human and even model organism phenotyping use case is more specific than what might be in PATO, and that PATO is a bit odd ;-). However, we need these terms to be used across the phenotype ontologies, so my suggestion is that they are imported into HPO regardless of how/where we specify them, so that we can have this consistency. I had thought that we could make an HPO specific slim that had the required labels and community-definitions in PATO (this is why I added them there), but of course this could be its own little vocabulary elsewhere as well. The main thing is to take a more modular approach so that we can have better interoperability across all the phenotype ontologies. I would not release anything in HPO until we can reconcile things next week, convenient timing!

-melissa

Original comment by: mellybelly