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

Michael Miller mmiller at teranode.com
Mon Apr 12 07:54:45 PDT 2010


hi trish,

thanks for the info--probably for the next version of annotare we should
leverage the widgets or the code behind them to allow a user to load an
existing MAE-TAB set of files and easily view the full definition of
ontology terms.

cheers,
michael

> -----Original Message-----
> From: annotare-dev at googlegroups.com [mailto:annotare-
> dev at googlegroups.com] On Behalf Of Trish Whetzel
> Sent: Saturday, April 10, 2010 1:50 PM
> To: mdmiller
> Cc: annotare-dev at googlegroups.com; support at bioontology.org
> Subject: Re: updates to designer wizard--units
>
> 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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> >>>
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> >>>            <tables_2009_11_13.txt>
> >>>
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> >>>
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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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