gusdev-gusdev

[Gusdev-gusdev] Sequence Type controlled vocab

[Steve F. <sfi...@pc...>]

folks-

in gus we have a Dots.SequenceType table.

here are the columns:
 nucleotide_type
 sub_type
 strand
 hierarchy    [should be hierarchy_depth]
 parent_sequence_type_id
 name
 description

First question:  does anybody know of an "emerging standard" for this?

If there is one, then we should include it in the Controlled Vocabs that 
we package with GUS.

Otherwise, we have, I think, two candidate SequenceTypeCVs:
   - the one provided by Sanger on the wiki:  
http://www.gusdb.org/wiki/index.php/Bootstrap%20data#ExternalDatabase
   - the one currently housed in CBIL's GUS instance

As part of the GUS 3.5 install, we are getting serious about making the 
loading of CVs much easier.   A central part of that is making the CVs 
available from CBIL's download site (eg, the CBIL anatomy CV).

So, i am thinking that CBIL should chose one (or more) sequence type CVs 
to provide as downloads.  They could be offered in GUS XML format.

Then, the automated GUS CV installer would find them from CBIL just like 
it will find GO from the GO Consortium.

Any plugin that uses SequenceTypes should *not* hard code the transform, 
but, instead, take a SequenceTypeMapping file.  The file specifies the 
mapping from input sequence type to that stored in gus (by name).  The 
plugin should pre-scan the input file to detect if there are any illegal 
sequence types, and warn the user before loading any data

If users find sequence types that the CBIL CV is missing, they can 
propose them via the mailing list.

The objective is to:
 1. work with the fact that different input files for a plugin may use 
different sequence types
 2. get out of the business of ad hoc changes to the sequence types 
stored in the db

comments?

steve

as a candidate CV the Sequence the SequenceTypesCV as developed by

If not, then, how about this.   Plugins that depend on sequence type use 
a standard config file for sequence type.  (this might apply to other 
loose CVs).  The config file specifies the

Re: [Gusdev-gusdev] Sequence Type controlled vocab

[Steve F. <sfi...@pc...>]

mike raises the point that the CV we publish should not be in GUS XML 
format, but, in a system neutral format.

then we would need a dedicated plugin like LoadCBILSequenceTypes that 
would read that format.

steve

Steve Fischer wrote:

> folks-
>
> in gus we have a Dots.SequenceType table.
>
> here are the columns:
> nucleotide_type
> sub_type
> strand
> hierarchy    [should be hierarchy_depth]
> parent_sequence_type_id
> name
> description
>
> First question:  does anybody know of an "emerging standard" for this?
>
> If there is one, then we should include it in the Controlled Vocabs 
> that we package with GUS.
>
> Otherwise, we have, I think, two candidate SequenceTypeCVs:
>   - the one provided by Sanger on the wiki:  
> http://www.gusdb.org/wiki/index.php/Bootstrap%20data#ExternalDatabase
>   - the one currently housed in CBIL's GUS instance
>
> As part of the GUS 3.5 install, we are getting serious about making 
> the loading of CVs much easier.   A central part of that is making the 
> CVs available from CBIL's download site (eg, the CBIL anatomy CV).
>
> So, i am thinking that CBIL should chose one (or more) sequence type 
> CVs to provide as downloads.  They could be offered in GUS XML format.
>
> Then, the automated GUS CV installer would find them from CBIL just 
> like it will find GO from the GO Consortium.
>
> Any plugin that uses SequenceTypes should *not* hard code the 
> transform, but, instead, take a SequenceTypeMapping file.  The file 
> specifies the mapping from input sequence type to that stored in gus 
> (by name).  The plugin should pre-scan the input file to detect if 
> there are any illegal sequence types, and warn the user before loading 
> any data
>
> If users find sequence types that the CBIL CV is missing, they can 
> propose them via the mailing list.
>
> The objective is to:
> 1. work with the fact that different input files for a plugin may use 
> different sequence types
> 2. get out of the business of ad hoc changes to the sequence types 
> stored in the db
>
> comments?
>
> steve
>
> as a candidate CV the Sequence the SequenceTypesCV as developed by
>
> If not, then, how about this.   Plugins that depend on sequence type 
> use a standard config file for sequence type.  (this might apply to 
> other loose CVs).  The config file specifies the
>
>
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> Tool for open source databases. Create drag-&-drop reports. Save time
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Re: [Gusdev-gusdev] Sequence Type controlled vocab

[Chris S. <sto...@pc...>]

Steve,
There are two complementary standards for sequence type. One comes from 
the MGED Ontology.
see 
http://mged.sourceforge.net/ontologies/MGEDontology.php#BioSequenceType
The other is SO  http://song.sourceforge.net/
Chris

On Feb 2, 2005, at 5:14 PM, Steve Fischer wrote:

> folks-
>
> in gus we have a Dots.SequenceType table.
>
> here are the columns:
> nucleotide_type
> sub_type
> strand
> hierarchy    [should be hierarchy_depth]
> parent_sequence_type_id
> name
> description
>
> First question:  does anybody know of an "emerging standard" for this?
>
> If there is one, then we should include it in the Controlled Vocabs 
> that we package with GUS.
>
> Otherwise, we have, I think, two candidate SequenceTypeCVs:
>   - the one provided by Sanger on the wiki:  
> http://www.gusdb.org/wiki/index.php/Bootstrap%20data#ExternalDatabase
>   - the one currently housed in CBIL's GUS instance
>
> As part of the GUS 3.5 install, we are getting serious about making 
> the loading of CVs much easier.   A central part of that is making the 
> CVs available from CBIL's download site (eg, the CBIL anatomy CV).
>
> So, i am thinking that CBIL should chose one (or more) sequence type 
> CVs to provide as downloads.  They could be offered in GUS XML format.
>
> Then, the automated GUS CV installer would find them from CBIL just 
> like it will find GO from the GO Consortium.
>
> Any plugin that uses SequenceTypes should *not* hard code the 
> transform, but, instead, take a SequenceTypeMapping file.  The file 
> specifies the mapping from input sequence type to that stored in gus 
> (by name).  The plugin should pre-scan the input file to detect if 
> there are any illegal sequence types, and warn the user before loading 
> any data
>
> If users find sequence types that the CBIL CV is missing, they can 
> propose them via the mailing list.
>
> The objective is to:
> 1. work with the fact that different input files for a plugin may use 
> different sequence types
> 2. get out of the business of ad hoc changes to the sequence types 
> stored in the db
>
> comments?
>
> steve
>
> as a candidate CV the Sequence the SequenceTypesCV as developed by
>
> If not, then, how about this.   Plugins that depend on sequence type 
> use a standard config file for sequence type.  (this might apply to 
> other loose CVs).  The config file specifies the
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting
> Tool for open source databases. Create drag-&-drop reports. Save time
> by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc.
> Download a FREE copy at http://www.intelliview.com/go/osdn_nl
> _______________________________________________
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Re: [Gusdev-gusdev] Sequence Type controlled vocab

[Steve F. <sfi...@pc...>]

folks-

Having looked at SO and MGED, I am not sure they are capturing what I 
have in mind, or, what we have captured in our SequenceType table

Here is the way I am thinking about breaking down "sequence type."   (If 
somebody can show me how these map into either of the ontologies Chris 
has mentioned that would be great).

For NA sequences:

Polymer Type
  - DNA
  - RNA
Molecule
  - chromosome
  - mRNA
  - tRNA
  - rRNA
  - oligo
Strandedness
  - single
  - double
Sequencing process
  - Genomic
  - EST
  - predicted
  - transcribed
  - what else?
Source
  - nucleus
  - mitochondria
  - plastid
  - plasmid
  - episome

Steve

Chris Stoeckert wrote:

> Steve,
> There are two complementary standards for sequence type. One comes 
> from the MGED Ontology.
> see 
> http://mged.sourceforge.net/ontologies/MGEDontology.php#BioSequenceType
> The other is SO  http://song.sourceforge.net/
> Chris
>
> On Feb 2, 2005, at 5:14 PM, Steve Fischer wrote:
>
>> folks-
>>
>> in gus we have a Dots.SequenceType table.
>>
>> here are the columns:
>> nucleotide_type
>> sub_type
>> strand
>> hierarchy    [should be hierarchy_depth]
>> parent_sequence_type_id
>> name
>> description
>>
>> First question:  does anybody know of an "emerging standard" for this?
>>
>> If there is one, then we should include it in the Controlled Vocabs 
>> that we package with GUS.
>>
>> Otherwise, we have, I think, two candidate SequenceTypeCVs:
>>   - the one provided by Sanger on the wiki:  
>> http://www.gusdb.org/wiki/index.php/Bootstrap%20data#ExternalDatabase
>>   - the one currently housed in CBIL's GUS instance
>>
>> As part of the GUS 3.5 install, we are getting serious about making 
>> the loading of CVs much easier.   A central part of that is making 
>> the CVs available from CBIL's download site (eg, the CBIL anatomy CV).
>>
>> So, i am thinking that CBIL should chose one (or more) sequence type 
>> CVs to provide as downloads.  They could be offered in GUS XML format.
>>
>> Then, the automated GUS CV installer would find them from CBIL just 
>> like it will find GO from the GO Consortium.
>>
>> Any plugin that uses SequenceTypes should *not* hard code the 
>> transform, but, instead, take a SequenceTypeMapping file.  The file 
>> specifies the mapping from input sequence type to that stored in gus 
>> (by name).  The plugin should pre-scan the input file to detect if 
>> there are any illegal sequence types, and warn the user before 
>> loading any data
>>
>> If users find sequence types that the CBIL CV is missing, they can 
>> propose them via the mailing list.
>>
>> The objective is to:
>> 1. work with the fact that different input files for a plugin may use 
>> different sequence types
>> 2. get out of the business of ad hoc changes to the sequence types 
>> stored in the db
>>
>> comments?
>>
>> steve
>>
>> as a candidate CV the Sequence the SequenceTypesCV as developed by
>>
>> If not, then, how about this.   Plugins that depend on sequence type 
>> use a standard config file for sequence type.  (this might apply to 
>> other loose CVs).  The config file specifies the
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting
>> Tool for open source databases. Create drag-&-drop reports. Save time
>> by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc.
>> Download a FREE copy at http://www.intelliview.com/go/osdn_nl
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting
> Tool for open source databases. Create drag-&-drop reports. Save time
> by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc.
> Download a FREE copy at http://www.intelliview.com/go/osdn_nl
> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [Gusdev-gusdev] Sequence Type controlled vocab

[Steve F. <sfi...@pc...>]

Aaron encouraged me to take a second look at SO.   (my first look came 
up dry, and i surmised that it was more "feature" oriented than 
"sequence" oriented)

the results are below

But first, here are the term in CBIL's SequenceType table:
DNA
RNA
ds-DNA
ss-DNA
ss-RNA
ds-RNA
mRNA
EST
tRNA
rRNA
unknown
predicted_mRNA
virtual
GSS
oligonucleotide

To, me, this is confuting multiple concepts: polymer type, strandedness, 
molecule

But, I am now thinking that if we replaced that list with the following 
attributes and values, we would probably be just fine.  SequenceType 
here *is* confuting multiple concepts, but, in a way that i think will 
satisfy intuition and reasonable querying needs:

  Singlestranded 
     true
     false
  SequenceType:
     chromosomal
     mRNA
     rRNA
     tRNA
     EST
     oligo
   HasPieces   (is virtual)
      true
      false   

Now for the SO survey:

Polymer Type   - no
  - DNA  - no
  - RNA - no

Molecule - no
 - chromosome  - SO:0000340
  - mRNA -  SO:0000234
  - tRNA -  SO:0000253
 - rRNA -  SO:0000252
 - oligo -  SO:0000696
Strandedness - no
 - single  - no
 - double  - no
Sequencing process   - derived_from
 - Genomic - no
 - EST  -  SO:0000345
 - predicted - no
 - transcribed - no
 - what else?
Source - no
 - nucleus  - no
 - mitochondria - no
 - plastid  - no
 - plasmid  - no
 - episome  - no

Guess what, all the sequence types in my proposed list above are found 
in the SO:
 - chromosome  - SO:0000340
  - mRNA -  SO:0000234
  - tRNA -  SO:0000253
 - rRNA -  SO:0000252
 - oligo -  SO:0000696
  - EST  -  SO:0000345

But, does that mean we should abolish the SequenceType table?    If we 
do, then a sequence would point to the SO for its type.   The advantage 
is that we will be out of the business of inventing yet another CV.   
The disadvantage is that now users have to wade through 400+ terms to 
find the 6 that we think are relevant

????

steve


Steve Fischer wrote:

> folks-
>
> Having looked at SO and MGED, I am not sure they are capturing what I 
> have in mind, or, what we have captured in our SequenceType table
>
> Here is the way I am thinking about breaking down "sequence type."   
> (If somebody can show me how these map into either of the ontologies 
> Chris has mentioned that would be great).
>
> For NA sequences:
>
> Polymer Type
>  - DNA
>  - RNA
> Molecule
>  - chromosome
>  - mRNA
>  - tRNA
>  - rRNA
>  - oligo
> Strandedness
>  - single
>  - double
> Sequencing process
>  - Genomic
>  - EST
>  - predicted
>  - transcribed
>  - what else?
> Source
>  - nucleus
>  - mitochondria
>  - plastid
>  - plasmid
>  - episome
>
> Steve
>
> Chris Stoeckert wrote:
>
>> Steve,
>> There are two complementary standards for sequence type. One comes 
>> from the MGED Ontology.
>> see 
>> http://mged.sourceforge.net/ontologies/MGEDontology.php#BioSequenceType
>> The other is SO  http://song.sourceforge.net/
>> Chris
>>
>> On Feb 2, 2005, at 5:14 PM, Steve Fischer wrote:
>>
>>> folks-
>>>
>>> in gus we have a Dots.SequenceType table.
>>>
>>> here are the columns:
>>> nucleotide_type
>>> sub_type
>>> strand
>>> hierarchy    [should be hierarchy_depth]
>>> parent_sequence_type_id
>>> name
>>> description
>>>
>>> First question:  does anybody know of an "emerging standard" for this?
>>>
>>> If there is one, then we should include it in the Controlled Vocabs 
>>> that we package with GUS.
>>>
>>> Otherwise, we have, I think, two candidate SequenceTypeCVs:
>>>   - the one provided by Sanger on the wiki:  
>>> http://www.gusdb.org/wiki/index.php/Bootstrap%20data#ExternalDatabase
>>>   - the one currently housed in CBIL's GUS instance
>>>
>>> As part of the GUS 3.5 install, we are getting serious about making 
>>> the loading of CVs much easier.   A central part of that is making 
>>> the CVs available from CBIL's download site (eg, the CBIL anatomy CV).
>>>
>>> So, i am thinking that CBIL should chose one (or more) sequence type 
>>> CVs to provide as downloads.  They could be offered in GUS XML format.
>>>
>>> Then, the automated GUS CV installer would find them from CBIL just 
>>> like it will find GO from the GO Consortium.
>>>
>>> Any plugin that uses SequenceTypes should *not* hard code the 
>>> transform, but, instead, take a SequenceTypeMapping file.  The file 
>>> specifies the mapping from input sequence type to that stored in gus 
>>> (by name).  The plugin should pre-scan the input file to detect if 
>>> there are any illegal sequence types, and warn the user before 
>>> loading any data
>>>
>>> If users find sequence types that the CBIL CV is missing, they can 
>>> propose them via the mailing list.
>>>
>>> The objective is to:
>>> 1. work with the fact that different input files for a plugin may 
>>> use different sequence types
>>> 2. get out of the business of ad hoc changes to the sequence types 
>>> stored in the db
>>>
>>> comments?
>>>
>>> steve
>>>
>>> as a candidate CV the Sequence the SequenceTypesCV as developed by
>>>
>>> If not, then, how about this.   Plugins that depend on sequence type 
>>> use a standard config file for sequence type.  (this might apply to 
>>> other loose CVs).  The config file specifies the
>>>
>>>
>>> -------------------------------------------------------
>>> This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting
>>> Tool for open source databases. Create drag-&-drop reports. Save time
>>> by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc.
>>> Download a FREE copy at http://www.intelliview.com/go/osdn_nl
>>> _______________________________________________
>>> Gusdev-gusdev mailing list
>>> Gus...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>
>>
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting
>> Tool for open source databases. Create drag-&-drop reports. Save time
>> by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc.
>> Download a FREE copy at http://www.intelliview.com/go/osdn_nl
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>
>

Re: [Gusdev-gusdev] Sequence Type controlled vocab

[Aaron J. M. <am...@pc...>]

First, I would encourage you to look at SOFA, the subset of SO useful 
for sequence annotation (which is presumably what you're doing, right?)

I would argue that these extra "attributes" you don't find explictly 
listed in SO are actually redundant to specific datatypes found in SO, 
i.e. these are encapsulated in the definition of each term.

On Feb 3, 2005, at 7:54 AM, Steve Fischer wrote:

> Polymer Type   - no
>  - DNA  - no
>  - RNA - no

an mRNA is RNA, not DNA; a chromosome is DNA, not RNA (unless its a 
viral genome, etc).

> Strandedness - no
> - single  - no
> - double  - no

ditto; strandness is inherent to the definition of a type

> Sequencing process   - derived_from
> - Genomic - no
> - EST  -  SO:0000345
> - predicted - no
> - transcribed - no
> - what else?

all of these are there, you just have to look for them in more 
biologically meaningful terms than what you have here.  and 
"derived_from" is not a SO term, it's a relationship type.

> Source - no
> - nucleus  - no
> - mitochondria - no
> - plastid  - no
> - plasmid  - no
> - episome  - no

ditto.

SO is/was designed to recapitulate biology (as best as possible), not 
the awkward attribute simplifications you seem to want to use (for 
instance, it seems in your scheme that I could have a sequence type 
that was DNA, mRNA, double stranded, predicted and episomal all at 
once).  With SO, you find the specific name for the thing you have ...

To put it in a more generic context: with SO you have "integer", 
"unsigned integer", "long integer", "unsigned long integer", "signed 
integer", etc., related in a hierarchy of isa/derived_from/part_of 
relationships; you don't have "signed" and "unsigned", "long" and 
"short", etc. as singular terms.  Now if you wanted to overlay a second 
ontology of term relationships (e.g. the "signedness" ontology), you 
could relate terms by these "attributes", and have the best of both 
worlds.

-Aaron

--
Aaron J. Mackey, Ph.D.
Dept. of Biology, Goddard 212
University of Pennsylvania       email:  am...@pc...
415 S. University Avenue         office: 215-898-1205
Philadelphia, PA  19104-6017     fax:    215-746-6697

Re: [Gusdev-gusdev] Sequence Type controlled vocab

[Angel P. <an...@ma...>]

Aaron,

I can't agree more with your points. Please keep up the good suggestions.

I thought a while back, GUS developers had agreed to replace CBIL's 
ad-hoc sequence ontology terms and gene models (not ad-hoc, but derived 
from EpoDB?) with SO as the major ontology for defining them. Makes 
sense to just extend the use of SO within GUS for all sequence 
categorizations.

The drawback I can see is the added layer of logic that developers must 
now know. For instance the WDK queries *may* become more complex, 
sequence annotation tools must now type sequences on defined terms, 
possibly a hierarchy of them. But since we are ditching the annot tool 
project that is not a concern. WDK queries writers would need to know 
the semantics of the current attribute model anyway, so it is not a 
stratch for them to learn sematics of SO and apply them. Also that new 
knowledge will be applicable to more than just a WDK query, so that is a 
win.

Two other advantages: 1) since it is widely accepted, most annotation 
tools should eventually provide native support for SO, and 2) we would 
more easily be able to share our gene models across GUS sites and othe 
non-GUS sites.


Angel

Aaron J. Mackey wrote:

> First, I would encourage you to look at SOFA, the subset of SO useful 
> for sequence annotation (which is presumably what you're doing, right?)
>
> I would argue that these extra "attributes" you don't find explictly 
> listed in SO are actually redundant to specific datatypes found in SO, 
> i.e. these are encapsulated in the definition of each term.
>
> On Feb 3, 2005, at 7:54 AM, Steve Fischer wrote:
>
>> Polymer Type   - no
>>  - DNA  - no
>>  - RNA - no
>
>
> an mRNA is RNA, not DNA; a chromosome is DNA, not RNA (unless its a 
> viral genome, etc).
>
>> Strandedness - no
>> - single  - no
>> - double  - no
>
>
> ditto; strandness is inherent to the definition of a type
>
>> Sequencing process   - derived_from
>> - Genomic - no
>> - EST  -  SO:0000345
>> - predicted - no
>> - transcribed - no
>> - what else?
>
>
> all of these are there, you just have to look for them in more 
> biologically meaningful terms than what you have here.  and 
> "derived_from" is not a SO term, it's a relationship type.
>
>> Source - no
>> - nucleus  - no
>> - mitochondria - no
>> - plastid  - no
>> - plasmid  - no
>> - episome  - no
>
>
> ditto.
>
> SO is/was designed to recapitulate biology (as best as possible), not 
> the awkward attribute simplifications you seem to want to use (for 
> instance, it seems in your scheme that I could have a sequence type 
> that was DNA, mRNA, double stranded, predicted and episomal all at 
> once).  With SO, you find the specific name for the thing you have ...
>
> To put it in a more generic context: with SO you have "integer", 
> "unsigned integer", "long integer", "unsigned long integer", "signed 
> integer", etc., related in a hierarchy of isa/derived_from/part_of 
> relationships; you don't have "signed" and "unsigned", "long" and 
> "short", etc. as singular terms.  Now if you wanted to overlay a 
> second ontology of term relationships (e.g. the "signedness" 
> ontology), you could relate terms by these "attributes", and have the 
> best of both worlds.
>
> -Aaron
>
> -- 
> Aaron J. Mackey, Ph.D.
> Dept. of Biology, Goddard 212
> University of Pennsylvania       email:  am...@pc...
> 415 S. University Avenue         office: 215-898-1205
> Philadelphia, PA  19104-6017     fax:    215-746-6697
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting
> Tool for open source databases. Create drag-&-drop reports. Save time
> by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc.
> Download a FREE copy at http://www.intelliview.com/go/osdn_nl
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>


-- 

Angel Pizarro
Director, Bioinformatics Facility
Institute for Translational Medicine and Therapeutics
University of Pennsylvania
806 BRB II/III
421 Curie Blvd.
Philadelphia, PA 19104-6160

P: 215-573-3736
F: 215-573-9004