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

Michael Miller mmiller at teranode.com
Thu May 6 09:28:39 PDT 2010


hi trish,

thanks for keeping up with this.  i think the services could really add a
lot of value to Annotare

> thanks michael, that helps. wrt to the documentation aspect, can you
> provide examples of how you would like to see this - either or both in
> the wiki and the XML Schema?

i'm not so concerned as to how the documentation is done, altho i think
the documentation can't be done entirely in the XML Schema (some elements
are repeatable and it depends on the context and the values of the
attributes to determine what the element in the context means).

usually when i've done this task as a developer it's looking at the code
that looks up terms and simply(!) translating how the code transfers the
information into the XML.

> also, are there some web services you
> would like to see documented first?

i'm thinking in the context of Annotare v2, so there are a few months
before that really gets going.

cheers,
michael

> -----Original Message-----
> From: Trish Whetzel [mailto:whetzel at stanford.edu]
> Sent: Monday, April 26, 2010 4:17 PM
> To: Michael Miller
> Cc: annotare-dev at googlegroups.com; support at bioontology.org
> Subject: Re: [bioontology-support] updates to designer wizard--units
>
> thanks michael, that helps. wrt to the documentation aspect, can you
> provide examples of how you would like to see this - either or both in
> the wiki and the XML Schema? also, are there some web services you
> would like to see documented first?
>
> trish
>
>
> On Apr 26, 2010, at 3:11 PM, Michael Miller wrote:
>
> > hi trish,
> >
> >> Is having an XML Schema document
> >> maintained by NCBO a requirement for your use of the Web services?
> >
> > my context is can annotare provide a way for a reader to get
> > information
> > on a term that appears in a MAGE-TAB document.
> >
> > one thing a XML Schema provides is a contract on what terms will
> > appear in
> > the answer so that a sensible, stable translation to a UI can be
> done.
> > for instance, even tho there are probably generic transformations to
> > show
> > arbitrary XML nicely on a webpage, i would think that i wouldn't
> > want to
> > show the <success> or <classBean> tags to the user.
> >
> > further, although i can make some good guesses on what will be
> > returned
> > looking at the examples on the website, without documentation,
> > that's all
> > they are, good guesses which may not cover all the possibilities.
> > this
> > would need to be provided by NCBO, since the XML Schema, as i
> > mentioned,
> > is too general.
> >
> > so, there is enough information to probably use the web services and
> > make
> > an adequate UI from the examples but as a developer, i'm uneasy not
> > having
> > a definitive guide to the contents of the XML.
> >
> > cheers,
> > michael
> >
> >> -----Original Message-----
> >> From: Trish Whetzel [mailto:whetzel at stanford.edu]
> >> Sent: Monday, April 26, 2010 10:51 AM
> >> To: Michael Miller
> >> Cc: annotare-dev at googlegroups.com; support at bioontology.org
> >> Subject: Re: [bioontology-support] updates to designer wizard--units
> >>
> >> We do occasionally make changes to the Web services. However our
> >> policy is that we announce these changes via the bioportal-announce
> >> mailing list prior to pushing these to production and provide a
> >> pointer to the Stage server where code updates can be tested. There
> >> are a number of applications that are using the Web services and our
> >> goal is to not break others code.  Given that the XML Schema
> document
> >> is provided by a third-party, we need to discuss how this will be
> >> maintained and documented. In the meantime, I'll check with Eamonn
> on
> >> getting an update to the XML Schema. Is having an XML Schema
> document
> >> maintained by NCBO a requirement for your use of the Web services?
> >>
> >> Trish
> >>
> >>
> >>
> >> On Apr 26, 2010, at 8:59 AM, Michael Miller wrote:
> >>
> >>> hi trish,
> >>>
> >>> thanks, that's useful (in fact the web site of services is quite
> >>> useful!).
> >>>
> >>> i noticed that the schema eamonn provided is quite generic without
> >>> comments so if an application wanted to display the returned
> >>> information,
> >>> the application wouldn't be able to tell the user what the fields
> >>> meant.
> >>> the values for the same elements nested at a different levels, such
> >> as
> >>> <data> or <relations>, might have different meaning.  that is, the
> >>> service
> >>> itself decides what information the generic elements will contain
> so
> >> a
> >>> little more documentation would be helpful.
> >>>
> >>> i also noticed that the examples don't actually follow the schema
> >>> and
> >>> would not validate.  for instance, the term services and
> >>> hierarchical
> >>> services examples have <ontologyVersionId> and <synonyms> elements
> >>> that
> >>> aren't in the schema and the instance services examples have
> >>> elements
> >>> <instanceBean> and <instanceType> that also aren't in the schema.
> >>>
> >>> that said, the examples are useful and the context does make it
> >>> visually
> >>> useful to display generically, i just would worry that the NCBO
> >>> services
> >>> might end up like the sequence databases that continually tweak
> >>> their
> >>> output format and break services, like biojava, that sit on top of
> >>> them.
> >>>
> >>> cheers,
> >>> michael
> >>>
> >>>> -----Original Message-----
> >>>> From: Trish Whetzel [mailto:whetzel at stanford.edu]
> >>>> Sent: Monday, April 26, 2010 12:16 AM
> >>>> To: Michael Miller
> >>>> Cc: annotare-dev at googlegroups.com; support at bioontology.org;
> >>>> mdmiller
> >>>> Subject: Re: [bioontology-support] updates to designer wizard--
> >>>> units
> >>>>
> >>>> The Web services and example output are listed here:
> >>>> http://www.bioontology.org/wiki/index.php/NCBO_REST_services
> >>>> .  Eamonn provided us with an XML Schema for the term and
> hierarchy
> >>>> web services:
> >>>>
> >>
> http://www.bioontology.org/wiki/index.php/NCBO_REST_services#XML_Schema
> >>>> _Definitions_for_the_REST_services
> >>>> .
> >>>>
> >>>> Trish
> >>>>
> >>>>
> >>>>
> >>>> On Apr 23, 2010, at 3:45 PM, Michael Miller wrote:
> >>>>
> >>>>> hi trish,
> >>>>>
> >>>>> thanks, that's along the lines i was thinking.  now the hope is
> >> that
> >>>>> the
> >>>>> information entered into the MAGE-TAB documents is enough to use
> >> the
> >>>>> services.
> >>>>>
> >>>>> the XML return format looks nice, is there documentation and/or a
> >>>>> XMLSchema describing it?
> >>>>>
> >>>>> cheers,
> >>>>> michael
> >>>>>
> >>>>>> -----Original Message-----
> >>>>>> From: Trish Whetzel [mailto:whetzel at stanford.edu]
> >>>>>> Sent: Tuesday, April 20, 2010 2:40 PM
> >>>>>> To: Michael Miller
> >>>>>> Cc: annotare-dev at googlegroups.com; support at bioontology.org;
> >>>>>> mdmiller
> >>>>>> Subject: Re: [bioontology-support] updates to designer wizard--
> >>>>>> units
> >>>>>>
> >>>>>> 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_serv
> >>>>>> ices
> >>>>>> ), 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
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>         --     You received this message because you are
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> >>>>>>>>>>>>>> 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.
> >>>>>>>>>>>>>>
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> >>>>>>>>>>>>>>      <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
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> 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>
> >>>>>>>>>>>>>>
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> >>>>>>>>>>>>>>      <mailto:annotare-dev at googlegroups.com>>.
> >>>>>>>>>>>>>>      To unsubscribe from this group, send email to
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> >>>>>>>>>>>>>>      <mailto:annotare-
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> >>>>>>>>>>>>>>      <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
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> >>>>>>>>>>>>>>  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>.
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> >>>>>>>>>>>>>>  annotare-dev+unsubscribe at googlegroups.com
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> >>>>>>>>>>>>>>  For more options, visit this group at
> >>>>>>>>>>>>>>  http://groups.google.com/group/annotare-dev?hl=en.
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> --     You received this message because you are
> >> subscribed
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> >>>>>>>>>>>>>> Groups "annotare developers mailing list" group.
> >>>>>>>>>>>>>> To post to this group, send email to annotare-
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> >>>>>>>>>>>>>> <mailto:annotare-dev at googlegroups.com>.
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> >>>>>>>>>>>>>> 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.
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> >>>>>>>> dev+unsubscribe at googlegroups.com
> >>>>>>>>>>> .
> >>>>>>>>>>> For more options, visit this group at
> >>>>>>>> http://groups.google.com/group/annotare-dev?hl=en
> >>>>>>>>>>> .
> >>>>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> _______________________________________________
> >>>>>>>>> bioontology-support mailing list
> >>>>>>>>> bioontology-support at lists.stanford.edu
> >>>>>>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-
> >>>>>>>>> support
> >>>>>>>>
> >>>>>>>> --
> >>>>>>>> You received this message because you are subscribed to the
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> >>>>>>>> http://groups.google.com/group/annotare-dev?hl=en.
> >>>>>>> _______________________________________________
> >>>>>>> bioontology-support mailing list
> >>>>>>> bioontology-support at lists.stanford.edu
> >>>>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-
> >>>>>>> support



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