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[bioontology-support] updates to designer wizard--units

Trish Whetzel whetzel at stanford.edu
Tue Apr 13 09:16:12 PDT 2010


The BioPortal Search takes both term names and IDs as input. The term- 
selection widget (http://bioportal.bioontology.org/ontologies/42488#widgets 
) uses the Search web service and has the option to return the term  
name, ID, or URI. There is javascript available for download on the  
widgets page if this widget suits your needs.

Trish


On Apr 13, 2010, at 6:57 AM, mdmiller wrote:

> hi junmin,
>
> that sounds good, i think you can even search for 'time unit' in  
> EFO, get UO:0000003, then look that up.
>
> cheers,
> michael
> ----- Original Message ----- From: "Junmin Liu"  
> <junmin at pcbi.upenn.edu>
> To: <annotare-dev at googlegroups.com>
> Cc: "mdmiller" <mdmiller53 at comcast.net>; <support at bioontology.org>
> Sent: Monday, April 12, 2010 7:00 PM
> Subject: Re: updates to designer wizard--units
>
>
>> Hi, Trish and Michael,
>> I can use the onotlogy search tool we have built into annotare on  
>> top of bioportal web service to search the term like UO:0000003.
>>
>> it gave me:
>> <searchResultList>
>>          <searchBean>
>>            <ontologyVersionId>42471</ontologyVersionId>
>>            <ontologyId>1112</ontologyId>
>>            <ontologyDisplayLabel>Units of measurement</ 
>> ontologyDisplayLabel>
>>            <recordType>RECORD_TYPE_CONCEPT_ID</recordType>
>>            <conceptId>UO:0000003</conceptId>
>>            <conceptIdShort>UO:0000003</conceptIdShort>
>>            <preferredName>time unit</preferredName>
>>            <contents>UO:0000003</contents>
>>          </searchBean>
>> .....
>>
>> So we have the function already, just a matter about how to link it  
>> up inside the application.
>>
>> Thanks,
>> --junmin
>>
>>
>> On Sat, 10 Apr 2010, Trish Whetzel wrote:
>>
>>> Hi Michael,
>>>
>>> There is a term-selection widget that BioPortal provides that  
>>> given a term name such as 'age', can return either the URI, term  
>>> id or preferred name for the term. The widgets page for EFO is at: http://bioportal.bioontology.org/ontologies/42488#widgets 
>>> . The BioPortal Web services can also be used to extract term  
>>> definitions to present back to the user.
>>>
>>> The Unit Ontology does exist as a separate ontology file, e.g. http://purl.bioontology.org/ontology/UO 
>>> . However, it seems as though in the broader context of sources  
>>> for unit terms this ontology is not mentioned. There is an effort  
>>> within the Ontolog group to work on a Quantity and Unit of Measure  
>>> Ontology-based Standard (http://ontolog.cim3.net/cgi-bin/wiki.pl? 
>>> UoM).
>>>
>>> Trish
>>>
>>>
>>> On Apr 10, 2010, at 9:00 AM, mdmiller wrote:
>>>
>>>> hi all,
>>>>
>>>> thanks for all the feedback, i'll use the EFO references.
>>>>
>>>> one question and more general comment, tho, referencing the term  
>>>> in a MAGE-TAB document seems incomplete.  there would be two  
>>>> approaches, the one i see in general is to use the label, for  
>>>> instance 'time unit'  and as the term source ref use EFO, which  
>>>> in the IDF has the URI (which is what i'll do).  but one nice  
>>>> feature is to be able to "link" to the definition  
>>>> programmatically, which this wouldn't allow.  from what's in the  
>>>> MAGE-TAB one would have to manually open up EFO in a browser,  
>>>> find 'time unit', go to OBO and use UO:0000003 to look it up.   
>>>> but having UO:0000003 as the value in MAGE-TAB is quite  
>>>> unfriendly for readability. so maybe for v2 of MAGE-TAB we allow  
>>>> a URN field for columns that can have terms from an ontology.  
>>>> granted, a bench scientist will probably not use that column but  
>>>> export applications at places like ArrayExpress could certainly  
>>>> add that.
>>>>
>>>> as a side, i went to check up more on the UNIT ONTOLOGY, i really  
>>>> didn't find much.
>>>>
>>>> found a great link that discusses the issue of units and  
>>>> ontologies and it mentions SI Units but not the Unit Ontology (as  
>>>> far as i can tell, i might have missed it).
>>>> the discussion is at http://groups.google.com/group/publishing-statistical-data/browse_thread/thread/80ca23044b6f1ea4 
>>>>  and richard cyganiak's answer is very detailed and fairly recent  
>>>> (march 10th).
>>>>
>>>> at the OBO site, UO is listed as part of PATO but the PATO wiki  
>>>> page doesn't seem to have much information on the units  
>>>> ontology.  all though OBO is a reputable site, there are other  
>>>> unit ontology efforts under way that do have documentation on  
>>>> their process, for instance the morfeo-project:
>>>>
>>>> http://forge.morfeo-project.org/wiki_en/index.php/Units_of_measurement_ontology
>>>>
>>>> cheers,
>>>> michael
>>>>
>>>> ----- Original Message ----- From: "James Malone"  
>>>> <malone at ebi.ac.uk>
>>>> To: "helen parkinson" <helen.parkinson at gmail.com>
>>>> Cc: <annotare-dev at googlegroups.com>
>>>> Sent: Friday, April 09, 2010 6:33 AM
>>>> Subject: Re: updates to designer wizard
>>>>
>>>>
>>>>> Yep, all in EFO, imported from Unit Ontology which is the  
>>>>> community authority and based on SI units.
>>>>>
>>>>> James
>>>>>
>>>>>
>>>>>
>>>>> helen parkinson wrote:
>>>>>> the units are all in EFO, where they have been imported from  
>>>>>> the units ontology, which is the authoritative source afaik -
>>>>>>
>>>>>> On Thu, Apr 8, 2010 at 9:21 PM, Joe White <jwhite at jimmy.harvard.edu 
>>>>>>  <mailto:jwhite at jimmy.harvard.edu>> wrote:
>>>>>>
>>>>>>   Hi Michael,
>>>>>>
>>>>>>   The units are probably in the EFO.  If not then there's the  
>>>>>> PATO
>>>>>>   Unit Ontology (if I remember the name correctly).
>>>>>>   Maybe this is helpful--if not obvious:
>>>>>>
>>>>>>   "age":  TimeUnit
>>>>>>   "dose",  ConcentrationUnit
>>>>>>   "irradiate", ?? (could be RAD or rem, but I don't think there  
>>>>>> was
>>>>>>   a unit class for this in MAGE)
>>>>>>   "temperature", TemperatureUnit (depending on source, it could  
>>>>>> be
>>>>>>   either deg C or deg F)
>>>>>>   "time",  TimeUnit
>>>>>>
>>>>>>   They are based on the old MAGE Unit classes though.
>>>>>>   Cheers,
>>>>>>   Joe
>>>>>>
>>>>>>   Ravi Shankar wrote:
>>>>>>
>>>>>>       No, she didn't.
>>>>>>
>>>>>>       On Apr 8, 2010, at 12:09 PM, Michael Miller wrote:
>>>>>>
>>>>>>           hi ravi,
>>>>>>
>>>>>>            excellent, this will help.  helen didn't include  
>>>>>> what type
>>>>>>           of units somewhere?
>>>>>>
>>>>>>            cheers,
>>>>>>           michael
>>>>>>
>>>>>>            *From:* annotare-dev at googlegroups.com
>>>>>>           <mailto:annotare-dev at googlegroups.com>
>>>>>>           <mailto:annotare-dev at googlegroups.com
>>>>>>           <mailto:annotare-dev at googlegroups.com>>
>>>>>>           [mailto:annotare-dev at googlegroups.com
>>>>>>           <mailto:annotare-dev at googlegroups.com>
>>>>>>           <mailto:annotare-dev at googlegroups.com
>>>>>>           <mailto:annotare-dev at googlegroups.com>>] *On Behalf Of
>>>>>>           *Ravi Shankar
>>>>>>
>>>>>>           *Sent:* Thursday, April 08, 2010 12:05 PM
>>>>>>           *To:* annotare-dev at googlegroups.com
>>>>>>           <mailto:annotare-dev at googlegroups.com>
>>>>>>           <mailto:annotare-dev at googlegroups.com
>>>>>>           <mailto:annotare-dev at googlegroups.com>>
>>>>>>           *Subject:* Re: updates to designer wizard
>>>>>>
>>>>>>
>>>>>>            Hi Michael,
>>>>>>           Here is are the lists that Helen gave me (a long while
>>>>>>           ago) that I am using for this purpose. Maybe, they  
>>>>>> need to
>>>>>>           be upgraded:
>>>>>>
>>>>>>            characteristicsTypes [ "age", "cell line", "cell  
>>>>>> type",
>>>>>>           "clinical history", "clinical treatment", "cultivar",
>>>>>>           "development stage", "disease location", "disease
>>>>>>           staging", "disease state", "ecology type",  
>>>>>> "enviromental
>>>>>>           history", "enviromental stress", "family history",
>>>>>>           "generation", "genetic modification", "genotype",  
>>>>>> "growth
>>>>>>           condition", "individual", "observation", "organism",
>>>>>>           "organism part", "performer", "phenotype",  
>>>>>> "population",
>>>>>>           "RNAi", "sex", "source provider", "strain or line"];
>>>>>>
>>>>>>            factorTypes ["age", "cell line", "cell type",  
>>>>>> "clinical
>>>>>>           history", "clinical treatment", "compound", "cultivar",
>>>>>>           "development stage", "disease location", "disease
>>>>>>           staging", "disease state", "dose", "ecology type",
>>>>>>           "enviromental history", "enviromental stress", "family
>>>>>>           history", "generation", "genetic modification",
>>>>>>           "genotype", "growth condition", "immunoprecipitate",
>>>>>>           "individual", "infect", "irradiate", "nutrients",
>>>>>>           "observation", "organism", "organism part",  
>>>>>> "performer",
>>>>>>           "phenotype", "population", "protocol", "replicate",
>>>>>>           "RNAi", "sex", "source provider", "strain or line",
>>>>>>           "temperature", "time"];
>>>>>>
>>>>>>            factorTypesWithUnits ["age", "dose", "irradiate",
>>>>>>           "temperature", "time"];
>>>>>>
>>>>>>            factorTypesWithOptionalUnits ["clinical treatment",
>>>>>>           "enviromental stress", "growth condition", "nutrients",
>>>>>>           "phenotype"];
>>>>>>
>>>>>>            factorTypesWithNoUnits ["cell line", "cell type",
>>>>>>           "clinical history", "clinical information", "compound",
>>>>>>           "developmental stage", "disease staging", "disease  
>>>>>> state",
>>>>>>           "genetic modification", "genotype",  
>>>>>> "immunoprecipitate",
>>>>>>           "individual", "infect", "organism", "organism part",
>>>>>>           "protocol", "sex", "strain or line"];
>>>>>>
>>>>>>            On Apr 8, 2010, at 6:40 AM, mdmiller wrote:
>>>>>>
>>>>>>
>>>>>>           hi rashmi,
>>>>>>
>>>>>>            thanks for the update.  i've included the file that  
>>>>>> has
>>>>>>           all the tables that drive the backend, the category  
>>>>>> table
>>>>>>           which translates to characteristics, organism,  
>>>>>> species and
>>>>>>           designs, which translates to experimental type, are
>>>>>>           directly from ArrayExpress.  modifying the tables that
>>>>>>           associate organism and categories and designs and
>>>>>>           categories will change the behavior of what the code  
>>>>>> will
>>>>>>           generate.
>>>>>>
>>>>>>            none of the changes require the Design Wizard UI be
>>>>>>           changed, except for perhaps a minor change.
>>>>>>
>>>>>>            "158: Default characteristic from template has no  
>>>>>> Unit column"
>>>>>>
>>>>>>            i will try and implement this over the weekend, i have
>>>>>>           guests so may have trouble getting it done.  it  
>>>>>> should be
>>>>>>           clear what characteristics have what units but see  
>>>>>> below
>>>>>>           for what i propose.
>>>>>>
>>>>>>            "120: Design Wizard should ask for experimental design
>>>>>>           type and not name."
>>>>>>
>>>>>>            issue 66: "Experiment Design Name doesn't default to  
>>>>>> type"
>>>>>>           is related to this and is marked as fixed--basically,  
>>>>>> this
>>>>>>           means if someone only selects a type, the name will
>>>>>>           default to the type.
>>>>>>
>>>>>>            if i remember right, both values are asked for,  
>>>>>> would it
>>>>>>           be better to have the type column first with the name
>>>>>>           column second?  or the UI might have changed since i  
>>>>>> last
>>>>>>           had a chance to take a look.
>>>>>>
>>>>>>            "149: SDRF should be located via reference in IDF  
>>>>>> file."
>>>>>>
>>>>>>            yes, in many discussions, this is always what has been
>>>>>>           agreed on.  in addition, if no SDRF file is listed, no
>>>>>>           attempt to find a default should be done.
>>>>>>
>>>>>>            "Issue 125
>>>>>>           <http://code.google.com/p/annotare/issues/detail? 
>>>>>> id=125>:
>>>>>>
>>>>>>                  Restrict array design selection based on vendor"
>>>>>>
>>>>>>            this is a duplicate of issue 61 and is marked
>>>>>>           critical,which is good.  this is why the design wizard
>>>>>>           exists--to make it easy for the user to select what  
>>>>>> they
>>>>>>           want.  if the choices aren't limited then the user is
>>>>>>           faced with many, many irrelevant choices in the  
>>>>>> dropdown.
>>>>>>            they should also be filtered by the species.
>>>>>>
>>>>>>            cheers,
>>>>>>           michael
>>>>>>
>>>>>>            here's what i see, not many characteristics will have
>>>>>>           units (and Time Units is listed as a characteristics  
>>>>>> which
>>>>>>           i'll probably remove).  the choices for units are
>>>>>>           TimeUnit, DistanceUnit, TemperatureUnit, QuantityUnit,
>>>>>>           MassUnit, VolumeUnit, and ConcentrationUnit:
>>>>>>
>>>>>>            display_label
>>>>>>                  unit
>>>>>>           Age
>>>>>>                  TimeUnit
>>>>>>           Organism part
>>>>>>                  Disease state
>>>>>>                  Cell line
>>>>>>                  Cell type
>>>>>>                  Developmental stage
>>>>>>                  Disease staging
>>>>>>                  Environmental history
>>>>>>                  Genetic modification
>>>>>>                  Histology
>>>>>>                  Individual
>>>>>>                  Genotype
>>>>>>                  Alive or dead?
>>>>>>                  Phenotype
>>>>>>                  Sex
>>>>>>                  Strain or line
>>>>>>                  Targeted cell type
>>>>>>                  Tumor grading
>>>>>>                  Ecotype
>>>>>>                  Clinical history
>>>>>>                  Time
>>>>>>                  TimeUnit
>>>>>>           Compound
>>>>>>                  Dose
>>>>>>                  VolumeUnit
>>>>>>           Species
>>>>>>                  Time Units
>>>>>>                  Initial Time Point
>>>>>>                  BioSource Provider
>>>>>>                  BioSource Type
>>>>>>                  fraction
>>>>>>                  GrowthCondition
>>>>>>                  RNAi
>>>>>>                  Growth condition
>>>>>>
>>>>>>              ----- Original Message -----
>>>>>>              *From:* Rashmi Srinivasa
>>>>>>           <mailto:rsrinivasa at 5amsolutions.com
>>>>>>           <mailto:rsrinivasa at 5amsolutions.com>>
>>>>>>              *To:* annotare-dev at googlegroups.com
>>>>>>           <mailto:annotare-dev at googlegroups.com>
>>>>>>              <mailto:annotare-dev at googlegroups.com
>>>>>>           <mailto:annotare-dev at googlegroups.com>>
>>>>>>              *Sent:* Tuesday, April 06, 2010 1:40 PM
>>>>>>              *Subject:* Fixes I'd like to see in v1.0
>>>>>>
>>>>>>              Hi everyone,
>>>>>>
>>>>>>              Out of the issues I entered, these are the ones I am
>>>>>>           hoping to
>>>>>>              see fixed in v1.0:
>>>>>>              120
>>>>>>            <http://code.google.com/p/annotare/issues/detail?id=120 
>>>>>> >:
>>>>>>           Design
>>>>>>
>>>>>>              Wizard should ask for experimental design type and  
>>>>>> not
>>>>>>           name.
>>>>>>              149
>>>>>>            <http://code.google.com/p/annotare/issues/detail?id=149 
>>>>>> >:
>>>>>>           SDRF
>>>>>>
>>>>>>              should be located via reference in IDF file.
>>>>>>              155
>>>>>>            <http://code.google.com/p/annotare/issues/detail?id=155 
>>>>>> >:
>>>>>>           Ontology
>>>>>>
>>>>>>              Search returns incorrect results for the MGED  
>>>>>> Ontology.
>>>>>>              158
>>>>>>            <http://code.google.com/p/annotare/issues/detail?id=158 
>>>>>> >:
>>>>>>           Default
>>>>>>
>>>>>>              characteristic from template has no Unit column.
>>>>>>              159
>>>>>>            <http://code.google.com/p/annotare/issues/detail?id=159 
>>>>>> >:
>>>>>>           Cannot
>>>>>>
>>>>>>              enter Unit columns for characteristics in SDRF  
>>>>>> Column
>>>>>>           Designer.
>>>>>>
>>>>>>              Thanks!
>>>>>>              Rashmi
>>>>>>              ---
>>>>>>              Rashmi Srinivasa, Ph.D.
>>>>>>              www.5amsolutions.com <http://www.5amsolutions.com>
>>>>>>           <http://www.5amsolutions.com> | Software for
>>>>>>              Life (TM)
>>>>>>              rsrinivasa at 5amsolutions.com
>>>>>>           <mailto:rsrinivasa at 5amsolutions.com>
>>>>>>           <mailto:rsrinivasa at 5amsolutions.com
>>>>>>           <mailto:rsrinivasa at 5amsolutions.com>>
>>>>>>
>>>>>>              434 825 4003
>>>>>>
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>>>>>> hl=en.
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>>>>>>           <tables_2009_11_13.txt>
>>>>>>
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>>>>>>
>>>>>>
>>>>>>
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>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> -- 
>>>>>> Helen Parkinson
>>>>>> Skype:helen.parkinson.ebi
>>>>>>
>>>>>
>>>>>
>>>>> -- 
>>>>> European Bioinformatics Institute, Wellcome Trust Genome Campus,  
>>>>> Hinxton, Cambridge, CB10 1SD, United Kingdom
>>>>> Tel: + 44 (0) 1223 494 676
>>>>> Fax: + 44 (0) 1223 492 468
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>>>>
>>>>
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