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

Trish Whetzel whetzel at stanford.edu
Mon Apr 26 16:17:00 PDT 2010


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
>>>>>>>>>>>>>>      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
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>>>>>>>>>>>>>>      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
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>>>>>>>>>>>>>>      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
>>>>>>>>>>> .
>>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> 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
>>>>>>>> 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.
>>>>>>> _______________________________________________
>>>>>>> bioontology-support mailing list
>>>>>>> bioontology-support at lists.stanford.edu
>>>>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology- 
>>>>>>> support




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