UMLS (Unified Medical Language System)

[Reagan Moore]

Roy:
Amarnath Gupta at SDSC has implemented the UMLS ontology in an Oracle 
database.  This is a collection of roughly 2 million terms and some 7 
million relationships.

The goal of the implementation was to understand scalability 
mechanisms for manipulating large ontologies, understand how to map 
the annotated relationships to logical rules, and understand how to 
apply the logical rules to query across collections with disparate 
semantic labels and attributes.

We have used the ontology for tasks such as:

- parse a report to identify relevant words
- use the UMLS ontology to identify a broader context that includes 
the identified words
- access the medpub collection to retrieve similar reports on the same subject.

Reagan


>I saw a link to this in my email this morning, the Unified Medical
>Language System (*), a compendium of different vocabularies about
>medicine. It is sorted and classified in different ways, and has
>licenced software to go with it.
>
>"The Metathesaurus preserves the meanings, attributes, hierarchical
>connections, and other relationships between terms present in its source
>vocabularies, while adding certain basic information about each of its
>concepts and establishing synonymy and new relationships between
>concepts and terms from different source vocabularies.
>
>METATHESAURUS SIZE: 113,699,627 BYTES.
>CONCEPT UNIQUE IDENTIFIERS (CUIs): 729,248
>SYNONYMS: 1,598,176
>
>I wonder if this is something we could develop as a VO resource? There
>are varous candidate vocabularies that we could uses as a basis listed
>below(**).
>
>It looks like NIH have spent a lot of resouces on UMLS, and I wonder
>exactly how people use it, and more importantly for us, how such a thing
>might help the VO community?
>
>Roy Williams
>---------
>Caltech Center for Advanced Computing Research
>mail    roy at cacr.caltech.edu
>voice   +1 626 395 3670
>
>
>-----------------------------------------------
>(*) The UMLS system is explained here:
>http://www.nlm.nih.gov/research/umls/META2.HTML
>
>This is a list of all the vocaularies that UMLS has subsumed
>http://www.nlm.nih.gov/research/umls/METAA1.HTML
>
>This is a list of "semantic types"
>http://umlsinfo.nlm.nih.gov/styfile.html
>
>-------------------------
>(**) Some Astronomy Vocabularies
>UCD vocabulary
>http://vizier.u-strasbg.fr/doc/UCD.htx
>
>Astronomy Thesaurus
>http://msowww.anu.edu.au/library/thesaurus/
>
>American Institute of Physics
>http://www.aip.org/pacs/pacs01/pacs0190.htm