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[bioontology-support] Fwd: Annotator support email list submission

Trish Whetzel whetzel at stanford.edu
Mon Jul 12 10:39:17 PDT 2010


Hi Misha 

Can you look into this question from Joey from our DBP with the Rat Genome Database?

I quickly used the Annotator last night and it seemed that hyphens were also being treated as word separators.  Has that always been the case? 

Thanks
Trish 


Sent from my iPhone

Begin forwarded message:

> From: Joey Geiger <jfgeiger at mcw.edu>
> Date: July 12, 2010 1:27:35 PM EDT
> To: Trish Whetzel <whetzel at stanford.edu>
> Subject: Annotator support email list submission
> 

> I don't remember what the support email was for the annotator (I re-installed my OS). I wanted to pass along something that I think is a bit odd.
> 
> When I try to parse the text "RatBrain_CTL_IBN_Rep1" it considers _ to be whitespace and breaks up the characters into chunks. Is there a way to get it to consider text with underlines to be considered complete words?
> 
> Results from the HTML version of the site is below so you can get my parameters. First is an actual request using the Cell Type. Next is a made up example using the rat strain ontology. While the term "SD" does appear in the text, since it's separated by "_" I would think that it should be considered a whole word.
> 
> Thanks.
> 
> 
> ObaResultBean [ 
> ResultBean [ 
>    resultID = OBA_RESULT_671a
>    dictionary = [id = 3, name = OBS_DICO_7281, dateCreated = 2009-06-17 16:19:47.0]
>    statistics = [(ISA_CLOSURE, 0) , (MAPPING, 2) , (MGREP, 0) ]
>    parameters = [longestOnly = false, wholeWordOnly = true, filterNumber = true, withSynonyms = true, scored = true, ontologiesToExpand = [], ontologiesToKeepInResult = [1006], isVirtualOntologyId = true, semanticTypes = [], levelMax = 0, mappingTypes = [], stopWords = [a, about, above, across, after, again, against, all, almost, alone, along, already, also, although, always, among, an, and, another, any, anybody, anyone, anything, anywhere, are, area, areas, around, as, ask, asked, asking, asks, at, away, b, back, backed, backing, backs, be, became, because, become, becomes, been, before, began, behind, being, beings, best, better, between, big, both, but, by, c, came, can, cannot, case, cases, certain, certainly, clear, clearly, come, could, d, did, differ, different, differently, do, does, done, down, down, downed, downing, downs, during, e, each, early, either, end, ended, ending, ends, enough, even, evenly, ever, every, everybody, everyone, everything, everywhere, f, face, faces, fact, facts, far, felt, few, find, finds, first, for, four, from, full, fully, further, furthered, furthering, furthers, g, gave, general, generally, get, gets, give, given, gives, go, going, good, goods, got, great, greater, greatest, group, grouped, grouping, groups, h, had, has, have, having, he, her, here, herself, high, high, high, higher, highest, him, himself, his, how, however, i, if, important, in, interest, interested, interesting, interests, into, is, it, its, itself, j, just, k, keep, keeps, kind, knew, know, known, knows, l, large, largely, last, later, latest, least, less, let, lets, like, likely, long, longer, longest, m, made, make, making, man, many, may, me, member, members, men, might, more, most, mostly, mr, mrs, much, must, my, myself, n, necessary, need, needed, needing, needs, never, new, new, newer, newest, next, no, nobody, non, noone, not, nothing, now, nowhere, number, numbers, o, of, off, often, old, older, oldest, on, once, one, only, open, opened, opening, opens, or, order, ordered, ordering, orders, other, others, our, out, over, p, part, parted, parting, parts, per, perhaps, place, places, point, pointed, pointing, points, possible, present, presented, presenting, presents, problem, problems, put, puts, q, quite, r, rather, really, right, right, room, rooms, s, said, same, saw, say, says, second, seconds, see, seem, seemed, seeming, seems, sees, several, shall, she, should, show, showed, showing, shows, side, sides, since, small, smaller, smallest, so, some, somebody, someone, something, somewhere, state, states, still, still, such, sure, t, take, taken, than, that, the, their, them, then, there, therefore, these, they, thing, things, think, thinks, this, those, though, thought, thoughts, three, through, thus, to, today, together, too, took, toward, turn, turned, turning, turns, two, u, under, until, up, upon, us, use, used, uses, v, very, w, want, wanted, wanting, wants, was, way, ways, we, well, wells, went, were, what, when, where, whether, which, while, who, whole, whose, why, will, with, within, without, work, worked, working, works, would, x, y, year, years, yet, you, young, younger, youngest, your, yours, z, et], withDefaultStopWords = false, isStopWordsCaseSenstive = false, text to annotate = RatBrain_CTL_IBN_Rep1]
> ]
>    ontologies = [[Cell type, nbAnnotation: 2, score: 14, (42768, 1.43, 1006)]]
>    annotations = [AnnotationBean [ 
>        score = 7
>        concept = [localConceptId: 42768/CL:0000794, conceptId: 7984493, localOntologyId: 42768, isTopLevel: 0, fullId: http://purl.obolibrary.org/obo/CL_0000794, preferredName: CD8-positive, alpha-beta cytotoxic T cell, definitions: [], synonyms: [cytotoxic T-lymphocyte, CD8-positive, alpha-beta cytotoxic T-lymphocyte, CD8-positive, alpha-beta cytotoxic T-cell, cytotoxic T-cell, cytotoxic T cell, cytotoxic T lymphocyte, CD8-positive, alpha-beta cytotoxic T lymphocyte], semanticTypes: [[id: 10675850, semanticType: T999, description: NCBO BioPortal concept]]]
>        context = [MAPPING(false), from = 10, to = 12, mappedConcept = [localConceptId: 42838/Cytotoxic_T-Lymphocyte, conceptId: 7913345, localOntologyId: 42838, isTopLevel: 0, fullId: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Cytotoxic_T-Lymphocyte, preferredName: Cytotoxic T-Lymphocyte, definitions: [], synonyms: [Cell-Mediated Lympholytic Cells, Cytotoxic T Cell, T-Lymphocytes, Cytotoxic, CTL, T-Lymphocyte, Cytotoxic, Cytotoxic T Cells, Cytolytic T-Cell, Cytotoxic T-Lymphocytes], semanticTypes: [[id: 10600838, semanticType: T025, description: Cell]]], mappingType = Automatic, ]
> ], AnnotationBean [ 
>        score = 7
>        concept = [localConceptId: 42768/CL:0000910, conceptId: 7984607, localOntologyId: 42768, isTopLevel: 0, fullId: http://purl.obolibrary.org/obo/CL_0000910, preferredName: cytotoxic T cell, definitions: [], synonyms: [cytotoxic T-lymphocyte, cytotoxic T-cell, cytotoxic T lymphocyte], semanticTypes: [[id: 10675964, semanticType: T999, description: NCBO BioPortal concept]]]
>        context = [MAPPING(false), from = 10, to = 12, mappedConcept = [localConceptId: 42838/Cytotoxic_T-Lymphocyte, conceptId: 7913345, localOntologyId: 42838, isTopLevel: 0, fullId: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Cytotoxic_T-Lymphocyte, preferredName: Cytotoxic T-Lymphocyte, definitions: [], synonyms: [Cell-Mediated Lympholytic Cells, Cytotoxic T Cell, T-Lymphocytes, Cytotoxic, CTL, T-Lymphocyte, Cytotoxic, Cytotoxic T Cells, Cytolytic T-Cell, Cytotoxic T-Lymphocytes], semanticTypes: [[id: 10600838, semanticType: T025, description: Cell]]], mappingType = Automatic, ]
> ]]
> ]
> 
> 
> ObaResultBean [ 
> ResultBean [ 
>    resultID = OBA_RESULT_7fa3
>    dictionary = [id = 3, name = OBS_DICO_7281, dateCreated = 2009-06-17 16:19:47.0]
>    statistics = [(MAPPING, 2) , (MGREP, 1) , (ISA_CLOSURE, 0) ]
>    parameters = [longestOnly = false, wholeWordOnly = true, filterNumber = true, withSynonyms = true, scored = true, ontologiesToExpand = [], ontologiesToKeepInResult = [1150], isVirtualOntologyId = true, semanticTypes = [], levelMax = 0, mappingTypes = [], stopWords = [a, about, above, across, after, again, against, all, almost, alone, along, already, also, although, always, among, an, and, another, any, anybody, anyone, anything, anywhere, are, area, areas, around, as, ask, asked, asking, asks, at, away, b, back, backed, backing, backs, be, became, because, become, becomes, been, before, began, behind, being, beings, best, better, between, big, both, but, by, c, came, can, cannot, case, cases, certain, certainly, clear, clearly, come, could, d, did, differ, different, differently, do, does, done, down, down, downed, downing, downs, during, e, each, early, either, end, ended, ending, ends, enough, even, evenly, ever, every, everybody, everyone, everything, everywhere, f, face, faces, fact, facts, far, felt, few, find, finds, first, for, four, from, full, fully, further, furthered, furthering, furthers, g, gave, general, generally, get, gets, give, given, gives, go, going, good, goods, got, great, greater, greatest, group, grouped, grouping, groups, h, had, has, have, having, he, her, here, herself, high, high, high, higher, highest, him, himself, his, how, however, i, if, important, in, interest, interested, interesting, interests, into, is, it, its, itself, j, just, k, keep, keeps, kind, knew, know, known, knows, l, large, largely, last, later, latest, least, less, let, lets, like, likely, long, longer, longest, m, made, make, making, man, many, may, me, member, members, men, might, more, most, mostly, mr, mrs, much, must, my, myself, n, necessary, need, needed, needing, needs, never, new, new, newer, newest, next, no, nobody, non, noone, not, nothing, now, nowhere, number, numbers, o, of, off, often, old, older, oldest, on, once, one, only, open, opened, opening, opens, or, order, ordered, ordering, orders, other, others, our, out, over, p, part, parted, parting, parts, per, perhaps, place, places, point, pointed, pointing, points, possible, present, presented, presenting, presents, problem, problems, put, puts, q, quite, r, rather, really, right, right, room, rooms, s, said, same, saw, say, says, second, seconds, see, seem, seemed, seeming, seems, sees, several, shall, she, should, show, showed, showing, shows, side, sides, since, small, smaller, smallest, so, some, somebody, someone, something, somewhere, state, states, still, still, such, sure, t, take, taken, than, that, the, their, them, then, there, therefore, these, they, thing, things, think, thinks, this, those, though, thought, thoughts, three, through, thus, to, today, together, too, took, toward, turn, turned, turning, turns, two, u, under, until, up, upon, us, use, used, uses, v, very, w, want, wanted, wanting, wants, was, way, ways, we, well, wells, went, were, what, when, where, whether, which, while, who, whole, whose, why, will, with, within, without, work, worked, working, works, would, x, y, year, years, yet, you, young, younger, youngest, your, yours, z, et], withDefaultStopWords = false, isStopWordsCaseSenstive = false, text to annotate = CHEESE_SD_BURGER]
> ]
>    ontologies = [[Rat Strain Ontology, nbAnnotation: 3, score: 24, (42515, 1.0, 1150)]]
>    annotations = [AnnotationBean [ 
>        score = 10
>        concept = [localConceptId: 42515/RS:0000681, conceptId: 4621708, localOntologyId: 42515, isTopLevel: 0, fullId: RS:0000681, preferredName: SD, definitions: [], synonyms: [RGD ID: 70508, Sprague Dawley , Sprague-Dawley], semanticTypes: [[id: 7217755, semanticType: T999, description: NCBO BioPortal concept]]]
>        context = [MGREP(true), from = 8, to = 9, [name: SD, localConceptId: 42515/RS:0000681, isPreferred: true, dictionaryId: 3], ]
> ], AnnotationBean [ 
>        score = 7
>        concept = [localConceptId: 42515/RS:0001409, conceptId: 4622434, localOntologyId: 42515, isTopLevel: 0, fullId: RS:0001409, preferredName: N:SD, definitions: [], synonyms: [SDN:SD, SD/N, RRRC:0239, Sprague-Dawley , Sprague Dawley ], semanticTypes: [[id: 7218481, semanticType: T999, description: NCBO BioPortal concept]]]
>        context = [MAPPING(false), from = 8, to = 9, mappedConcept = [localConceptId: 42838/Sudan, conceptId: 7960454, localOntologyId: 42838, isTopLevel: 0, fullId: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Sudan, preferredName: Sudan, definitions: [], synonyms: [SU, SDN, 736, SD], semanticTypes: [[id: 10650950, semanticType: T083, description: Geographic Area]]], mappingType = Automatic, ]
> ], AnnotationBean [ 
>        score = 7
>        concept = [localConceptId: 42515/RS:0000706, conceptId: 4621733, localOntologyId: 42515, isTopLevel: 0, fullId: RS:0000706, preferredName: SDT.ZDF-Leprfa/Jtt, definitions: [], synonyms: [RGD ID: 2314027, SDT.Cg-Leprfa/Jtp, SDT fatty], semanticTypes: [[id: 7217780, semanticType: T999, description: NCBO BioPortal concept]]]
>        context = [MAPPING(false), from = 8, to = 9, mappedConcept = [localConceptId: 42838/Sudan, conceptId: 7960454, localOntologyId: 42838, isTopLevel: 0, fullId: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Sudan, preferredName: Sudan, definitions: [], synonyms: [SU, SDN, 736, SD], semanticTypes: [[id: 10650950, semanticType: T083, description: Geographic Area]]], mappingType = Automatic, ]
> ]]
> ]
> 
> 

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