Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

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

mdmiller mdmiller53 at comcast.net
Tue Apr 13 06:57:46 PDT 2010


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
>>>>>
>>>>>               --     You received this message because you are
>>>>>            subscribed to the
>>>>>               Google Groups "annotare developers mailing list" group.
>>>>>               To post to this group, send email
>>>>>               to annotare-dev at googlegroups.com
>>>>>            <mailto:annotare-dev at googlegroups.com>
>>>>>               <mailto:annotare-dev at googlegroups.com
>>>>>            <mailto:annotare-dev at googlegroups.com>>.
>>>>>
>>>>>               To unsubscribe from this group, send email
>>>>>               to annotare-dev+unsubscribe at googlegroups.com
>>>>>            <mailto:annotare-dev%2Bunsubscribe at googlegroups.com>
>>>>>               <mailto:annotare-dev+unsubscribe at googlegroups.com
>>>>>            <mailto:annotare-dev%2Bunsubscribe at googlegroups.com>>.
>>>>>
>>>>>               For more options, visit this group
>>>>>               at http://groups.google.com/group/annotare-dev?hl=en.
>>>>>
>>>>>             --             You received this message because you are 
>>>>> subscribed to
>>>>>            the Google Groups "annotare developers mailing list" group.
>>>>>            To post to this group, send email to
>>>>>            annotare-dev at googlegroups.com
>>>>>            <mailto:annotare-dev at googlegroups.com>
>>>>>            <mailto:annotare-dev at googlegroups.com
>>>>>            <mailto:annotare-dev at googlegroups.com>>.
>>>>>            To unsubscribe from this group, send email to
>>>>>            annotare-dev+unsubscribe at googlegroups.com
>>>>>            <mailto:annotare-dev%2Bunsubscribe at googlegroups.com>
>>>>>            <mailto:annotare-dev+unsubscribe at googlegroups.com
>>>>>            <mailto:annotare-dev%2Bunsubscribe at googlegroups.com>>.
>>>>>
>>>>>            For more options, visit this group at
>>>>>            http://groups.google.com/group/annotare-dev?hl=en.
>>>>>            <tables_2009_11_13.txt>
>>>>>
>>>>>             --             You received this message because you are 
>>>>> subscribed to
>>>>>            the Google Groups "annotare developers mailing list" group.
>>>>>            To post to this group, send email to
>>>>>            annotare-dev at googlegroups.com
>>>>>            <mailto:annotare-dev at googlegroups.com>
>>>>>            <mailto:annotare-dev at googlegroups.com
>>>>>            <mailto:annotare-dev at googlegroups.com>>.
>>>>>            To unsubscribe from this group, send email to
>>>>>            annotare-dev+unsubscribe at googlegroups.com
>>>>>            <mailto:annotare-dev%2Bunsubscribe at googlegroups.com>
>>>>>            <mailto:annotare-dev%2Bunsubscribe at googlegroups.com
>>>>>            <mailto:annotare-dev%252Bunsubscribe at googlegroups.com>>.
>>>>>
>>>>>            For more options, visit this group at
>>>>>            http://groups.google.com/group/annotare-dev?hl=en.
>>>>>
>>>>>
>>>>>
>>>>>        --         You received this message because you are subscribed 
>>>>> to the
>>>>>        Google Groups "annotare developers mailing list" group.
>>>>>        To post to this group, send email to
>>>>>        annotare-dev at googlegroups.com
>>>>>        <mailto:annotare-dev at googlegroups.com>.
>>>>>        To unsubscribe from this group, send email to
>>>>>        annotare-dev+unsubscribe at googlegroups.com
>>>>>        <mailto:annotare-dev%2Bunsubscribe at googlegroups.com>.
>>>>>        For more options, visit this group at
>>>>>        http://groups.google.com/group/annotare-dev?hl=en.
>>>>>
>>>>>
>>>>>
>>>>>    --     You received this message because you are subscribed to the 
>>>>> Google
>>>>>    Groups "annotare developers mailing list" group.
>>>>>    To post to this group, send email to annotare-dev at googlegroups.com
>>>>>    <mailto:annotare-dev at googlegroups.com>.
>>>>>    To unsubscribe from this group, send email to
>>>>>    annotare-dev+unsubscribe at googlegroups.com
>>>>>    <mailto:annotare-dev%2Bunsubscribe at googlegroups.com>.
>>>>>    For more options, visit this group at
>>>>>    http://groups.google.com/group/annotare-dev?hl=en.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> -- 
>>>>> 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
>>>> -- 
>>>> You received this message because you are subscribed to the Google 
>>>> Groups "annotare developers mailing list" group.
>>>> To post to this group, send email to annotare-dev at googlegroups.com.
>>>> To unsubscribe from this group, send email to 
>>>> annotare-dev+unsubscribe at googlegroups.com.
>>>> For more options, visit this group at 
>>>> http://groups.google.com/group/annotare-dev?hl=en.
>>>>
>>>
>>>
>>
>> -- 
>> You received this message because you are subscribed to the Google Groups 
>> "annotare developers mailing list" group.
>> To post to this group, send email to annotare-dev at googlegroups.com.
>> To unsubscribe from this group, send email to 
>> annotare-dev+unsubscribe at googlegroups.com.
>> For more options, visit this group at 
>> http://groups.google.com/group/annotare-dev?hl=en.
>>
> 





More information about the bioontology-support mailing list