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

Michael Miller mmiller at teranode.com
Tue Apr 20 12:19:59 PDT 2010


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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> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> --
> >>>>>> 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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> >>>
> >
> >
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