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

Trish Whetzel whetzel at stanford.edu
Sat Apr 10 13:49:44 PDT 2010


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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