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

Trish Whetzel whetzel at stanford.edu
Tue Apr 20 14:40:29 PDT 2010


Hi Michael,

We are working to provide a SPARQL endpoint. In addition, depending on  
what information you have about a term, the application can generate a  
call to the Term Web service (http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Term_services 
), where the definition can be parsed out OR generate a link to the  
BioPortal 'visualize' page. All ontologies can be accessed via: http://purl.bioontology.org/ontology/OntologyAbbreviation/TermId 
. For example, http://purl.bioontology.org/ontology/EFO/EFO_0002029.

Trish


On Apr 20, 2010, at 12:19 PM, Michael Miller wrote:

> hi trish,
>
> another point here on my use case, is that it is for a reader of the
> MAGE-TAB document, not an annotator.  the tools you point out are  
> great
> for an annotator but a reader simply wants the info quickly and  
> easily.
>
> if the reader wanted to understand more about a characteristic, one  
> click
> should bring up a page with the full definition.
>
> so ideally the application can put together a sparql query or a URL  
> from
> the value in the characteristic column and its term source ref to  
> get this
> information then display it to the reader.
>
> i don't see that the current usage in MAGE-TAB supports this use case
> easily.
>
> cheers,
> michael
>
>> -----Original Message-----
>> From: annotare-dev at googlegroups.com [mailto:annotare-
>> dev at googlegroups.com] On Behalf Of Trish Whetzel
>> Sent: Tuesday, April 13, 2010 9:16 AM
>> To: mdmiller
>> Cc: Junmin Liu; annotare-dev at googlegroups.com;  
>> support at bioontology.org
>> Subject: Re: [bioontology-support] updates to designer wizard--units
>>
>> 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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>>>>>>>>          <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
>>>>>>> Tel: + 44 (0) 1223 494 676
>>>>>>> Fax: + 44 (0) 1223 492 468
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>>>>>>
>>>>>>
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