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[bioontology-support] FW: Feedback

Lau, William (NIH/CIT) [E] lauwill at mail.nih.gov
Thu Feb 25 13:24:40 PST 2010


I wasn't sure if my earlier email was sent out correctly.



Thanks for your attention.



William



From: Lau, William (NIH/CIT) [E]
Sent: Tuesday, February 23, 2010 7:48 PM
To: 'Trish Whetzel'
Subject: RE: [bioontology-support] Feedback



Hi Trish,



Thanks for your quick response. Here is a sample input:

"Cloning and characterization of two cytoplasmic dynein intermediate chain genes in mouse and human."



I am using the default parameters except for ontologyToKeepInResult, which I put in:  "42142,39966,42331,42333,40659,42303,42332,42165,42334"



I am getting XML output, but for readability, I am pasting less than 5% of the text output below.



There are a few issues:

(1)    As you can see,  the first two AnnotationBean objects are exactly the same. There are many of these in fact, which makes the output very very large due to the redundancy, and as a result, takes a long time to process.

(2)    In the previous version, I remember the term "human" mapped to MSH, but now it doesn't. It seems to be true for other ontologies as well too. Only some ontologies are working.

(3)    The localConceptId for some terms are now the term name. NCIt, for example, the localConceptId for human is 42331/Human, instead of 42331/C14225, which is the actual identifier in the ontology. In the old version, the UMLS CUIs are used as Ids. I can use it to translate to the naïve Id, but now it's not as easy.



Please let me know if you have solutions for these issues or bugs.



Thanks much,

William





ObaResultBean [
ResultBean [
        resultID = OBA_RESULT_da43
        dictionary = [id = 3, name = OBS_DICO_7281, dateCreated = 2009-06-17 16:19:47.0]
        statistics = [(MAPPING, 54) , (ISA_CLOSURE, 0) , (MGREP, 60) ]
        parameters = [longestOnly = false, wholeWordOnly = true, filterNumber = true, withSynonyms = true, scored = true, ontologiesToExpand = [], ontologiesToKeepInResult = [42142, 39966, 42331, 42333, 40659, 42303, 42332, 42165, 42334], isVirtualOntologyId = false, semanticTypes = [], levelMax = 0, mappingTypes = [], stopWords = [], withDefaultStopWords = false, isStopWordsCaseSenstive = false, text to annotate = Cloning and characterization of two cytoplasmic dynein intermediate chain genes in mouse and human. ]
]
        ontologies = [[NCI Thesaurus, nbAnnotation: 83, score: 5616, (42331, 09.09, 1032)], [Foundational Model of Anatomy, nbAnnotation: 23, score: 1704, (39966, 3.0, 1053)], [Gene Ontology, nbAnnotation: 8, score: 192, (42332, 1.794, 1070)]]
        annotations = [AnnotationBean [
               score = 132
               concept = [localConceptId: 42331/Human, conceptId: 3183531, localOntologyId: 42331, isTopLevel: 0, preferredName: Human, synonyms: [Human, General, Homo sapiens], semanticTypes: [[id: 4962845, semanticType: T999, description: NCBO BioPortal concept], [id: 4992520, semanticType: T016, description: Human]]]
               context = [MAPPING(false), mappedConceptID = 40739/p11:birnlex_516, mappingType = Automatic, termName = Human, from = 94, to = 98]
], AnnotationBean [
               score = 132
               concept = [localConceptId: 42331/Human, conceptId: 3183531, localOntologyId: 42331, isTopLevel: 0, preferredName: Human, synonyms: [Human, General, Homo sapiens], semanticTypes: [[id: 4962845, semanticType: T999, description: NCBO BioPortal concept], [id: 4992520, semanticType: T016, description: Human]]]
               context = [MAPPING(false), mappedConceptID = 40739/p11:birnlex_516, mappingType = Automatic, termName = Human, from = 94, to = 98]
],







From: Trish Whetzel [mailto:whetzel at stanford.edu]
Sent: Tuesday, February 23, 2010 6:58 PM
To: Lau, William (NIH/CIT) [E]
Cc: support at bioontology.org
Subject: Re: [bioontology-support] Feedback



Dear Dr. Lau,



Can you provide an example of the input text, parameters, and output you are using?



Thanks,

Trish





On Feb 23, 2010, at 3:21 PM, admin at bioontology.org<mailto:admin at bioontology.org> wrote:



Name : William Lau

Email : william.lau at nih.gov<mailto:william.lau at nih.gov>

Comment:
I'm using the Annotator REST service, but there are several bugs. First, the same terms are returned many many times. The xml output is very large even for one sentence. From what I can tell the the data are the same, just get repeated a lot. That slows down the performance dramatically. Also, it doesn't seem to be able to identify MeSH concepts.

I am not sure if the observations that I see are effects of the upgrade to version 2.3.
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Trish Whetzel, PhD

Outreach Coordinator

The National Center for Biomedical Ontology

Ph: 650-721-2378

whetzel at stanford.edu<mailto:whetzel at stanford.edu>

http://www.bioontology.org







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