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[bioontology-support] Filtering by semantic types with the Annotator
Clement Jonquet
jonquet at lirmm.fr
Thu Jul 17 08:17:48 PDT 2014
Hi Paul,
The thing is that the REST API offers only what has been parsed by the
umls2rdf tool and the hierarchy is not complete.
For instance:
http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioonto
logy.org%2Fontology%2FSTY%2FT077
has for ancestor:
http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioonto
logy.org%2Fontology%2FSTY%2FT077/ancestors
but has empty descendants while the SN defines:
Conceptual Entity
Idea or Concept
Temporal Concept
Qualitative Concept
Quantitative Concept
Functional Concept
Body System
Spatial Concept
Body Space or Junction
Body Location or Region
Molecular Sequence
Nucleotide Sequence
Amino Acid Sequence
Carbohydrate Sequence
Geographic Area
The information is only in the files here:
http://semanticnetwork.nlm.nih.gov/Download/
Clement
De : Paul R Alexander [mailto:palexander at stanford.edu]
Envoyé : samedi 12 juillet 2014 00:51
À : Clement Jonquet
Cc : bioportal; Nigam Shah
Objet : Re: [bioontology-support] Filtering by semantic types with the
Annotator
Clement,
Ive added an issue to investigate supporting the use of the Semantic Type
hierarchy when filtering. One easy fix is to use the descendants from the
REST API for a given Semantic Type class as input for the existing filter.
Paul
On Jul 10, 2014, at 7:45 AM, Clement Jonquet <jonquet at lirmm.fr
<mailto:jonquet at lirmm.fr> > wrote:
Hi all,
This is a bug or feature request depending on the point of views ;)
The UMLS Semantic Network (STY in BioPortal) is not parsed completely:
<http://bioportal.bioontology.org/ontologies/STY>
http://bioportal.bioontology.org/ontologies/STY
Especially the hierarchy as described here:
<http://www.nlm.nih.gov/research/umls/META3_current_semantic_types.html>
http://www.nlm.nih.gov/research/umls/META3_current_semantic_types.html
is not included.
Therefore, when filtering annotation with semantic types, the hierarchy
knowledge of the Semantic Network cannot be used.
For instance:
When annotating melanoma and filtering with T147:Disease or syndrome I
should get an annotation with
<http://bioportal.bioontology.org/ontologies/SNOMEDCT?p=classes&conceptid=ht
tp%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F2092003>
http://bioportal.bioontology.org/ontologies/SNOMEDCT?p=classes&conceptid=htt
p%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F2092003 which is
Malignant melanoma in SNOMEDCT that actually has T191 (neoplastic process)
which is defined in the UMLS SN has a subtype of T147.
Currently the Annotator does not match anything if filtering with T147 is
on.
Of course this should work also with all the parents in the hierarchy.
I see 2 bugs to fix:
- Parse the UMLS SN completely (has issued at:
<https://github.com/ncbo/umls2rdf/issues/9>
https://github.com/ncbo/umls2rdf/issues/9)
- Change Annotator code to use that hierarchy when filtering
Hope it helps
Clement
PS: as soon as I get a developer in Montpellier, we will do it ;)
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Dr. Clement JONQUET - PhD in Informatics - Assistant Professor
PI of the SIFR project <http://www.lirmm.fr/sifr/> : Semantic Indexing of
French Biomedical Data Resources (ANR, UM2, CNRS, IBC)
Organizer of Web Science Montpellier
<http://www.meetup.com/webscience-montpellier/> Meetup
jonquet at lirmm.fr <mailto:jonquet at lirmm.fr>
http://www.lirmm.fr/~jonquet
University of Montpellier Tel:
+33/4 67 14 97 43
LIRMM
Fax: +33/4 67 41 85 00
161 rue Ada
Skype: clementpro
34095 Montpellier Cdx 5 Twitter:
@jonquet_lirmm <http://twitter.com/jonquet_lirmm>
France
Google: jonquet.lirmm at gmail.com
<mailto:jonquet.lirmm at gmail.com>
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