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

Junmin Liu junmin at pcbi.upenn.edu
Mon Apr 12 19:00:25 PDT 2010


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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>>>>            <tables_2009_11_13.txt>
>>>> 
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>>>> 
>>>> 
>>>> 
>>>> -- 
>>>> Helen Parkinson
>>>> Skype:helen.parkinson.ebi
>>>> 
>>> 
>>> 
>>> -- 
>>> European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, 
>>> Cambridge, CB10 1SD, United Kingdom
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