gusdev-gusdev

[Gusdev-gusdev] DNA, RNA and Protein GUS Features + PeptidePropertyType Table

[Arnaud K. <ax...@sa...>]

Hi

I've attached the SQL statements for new views/tables in GUS3, as well 
as updates of existing views/tables. It covers a new sequence object and 
new DNA, RNA and protein features that we would like to use. Some of 
them have been designed to go along Sequence Ontology classification 
(see below).

Here a summary of the list of new views or tables:

Updated views/tables:
   * NAFeatureImp - modified:
      * name from varchar2(30) to varchar2(50)
   * RestrictionFragmentFeature - added:
      * type_of_cut (sticky or blunt)
   * SignalPeptideFeature - added:
      * targetting
   * GeneSynonym - added:
      * is_obsolete

New views/tables:

A new sequence object on the top of NASequenceImp:
   * GenomicSequence

New views on the top of NAFeatureImp:
   * ChromosomeElement
NB : (centromere, telomere => SO)
   * InflectionPointFeature
   * RepeatFeature
NB : repeat type => SO
   * RepeatRegionFeature
   * ReplicationFeature
   * TransposableElementFeature
NB: SO would give the type
   * RNARegulatory
   * RNASecondaryStructure
   * SpliceSiteFeature

New views on the top of AAFeatureImp:
   * AASecondaryStructure
   * AATertiaryStructure
   * DomainFeature
   * PeptideProperty
   * PostTranslationModification
   * TransmembraneDomainFeature

A new table:
   * PeptidePropertyType


Note that the design takes into account the use of the Sequence Ontology 
(SO) to refine the types of some the features, eg to differentiate the 
different types of transposable elements, of repeats or of chromosome 
elements (centromere, telomere ...).

e.g. Transposable Elements annotations:

The different types of transposable elements would be given by specific 
SO terms. Bear in mind the procaryotes transposable elements are not 
covered by SO, but we are working on addings SO procaryotes specific terms.

Here the current SO tree for transposable elements:

Transposable Element
   ---> Non Retrotransposon
           ---> TIR Element
                   ----> Terminal Inverted Repeat
           ---> Foldback Element
  ---> Retrotransposon
           ---> LTR Retrotransposon
                  ----> Long Terminal Repeat
           ---> non LTR Retrotransposon
                 ----> LINE Element
                 ----> SINE Element

LTRs, as well as genes, part of a transposable element would be features 
attached to a TransposableElement Feature. These genes would have the 
following SO term : transposable element gene, SO0000111.
Regarding LTRs, they will be considered as Repeat Feature, annotated 
with the right Sequence Ontology terms.

Let me know if you have any comments.

cheers
Arnaud

PS: Sequence Ontology URL

=> http://www.geneontology.org/gobo/sequence.ontology/sequence.ontology

Re: [Gusdev-gusdev] DNA, RNA and Protein GUS Features + PeptidePropertyType Table

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

Hi Arnaud,
Many thanks for compiling this. Just wanted to let you know that both 
Jonathan Crabtree and I plan to go through them to see if there are any 
proposals that require further discussion. Everyone else is encouraged 
to do so as well.
Cheers,
Chris

On Tuesday, October 8, 2002, at 09:00 AM, Arnaud Kerhornou wrote:

> Hi
>
> I've attached the SQL statements for new views/tables in GUS3, as well 
> as updates of existing views/tables. It covers a new sequence object 
> and new DNA, RNA and protein features that we would like to use. Some 
> of them have been designed to go along Sequence Ontology 
> classification (see below).
>
> Here a summary of the list of new views or tables:

Re: [Gusdev-gusdev] DNA, RNA and Protein GUS Features + PeptidePropertyType Table

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

Hi Arnaud,
I finally went through your list. These will certainly enrich GUS! Some 
questions/issues though.
First a general request for documentation of the tables and attributes 
to explain what they are to be used for. We have a plug-in that takes a 
file in the format:

TableName\t\tdescription
TableName\tAttributeName\tDescription

In particular, I am curious as to what InflectionPointFeature and 
ReplicationFeature are.

For the NAFeature views you propose, are you using "source_id" to point 
to SRes:SequenceOntology? If so, why not call the attribute "so_id"?
Similarly, for GenomeSequence as a view of NASequence, is this what 
"source_id" is for?

The AAFeature views have "name" attributes and I wonder whether we 
should have a table in SRes for controlled vocabulary terms for protein 
features that we can point to (as with sequence ontology). This would 
avoid the uncontrolled use of "name." I notice that PeptideProperty has 
been given a controlled vocabulary table PeptidePropertyType in this 
regard. Rather than have a table for each, we could centralize them. 
Any choices for the resource to use for these names? SWISS-PROT?

Cheers,
Chris

On Tuesday, October 8, 2002, at 09:00 AM, Arnaud Kerhornou wrote:

> From: Arnaud Kerhornou <ax...@sa...>
> Date: Tue Oct 8, 2002  9:00:32 AM US/Eastern
> To: gusdev-gusdev <gus...@li...>, 
> gen...@li...
> Subject: [Gusdev-gusdev] DNA, RNA and Protein GUS Features + 
> PeptidePropertyType Table
>
> Hi
>
> I've attached the SQL statements for new views/tables in GUS3, as well 
> as updates of existing views/tables. It covers a new sequence object 
> and new DNA, RNA and protein features that we would like to use. Some 
> of them have been designed to go along Sequence Ontology 
> classification (see below).
>
> Here a summary of the list of new views or tables:
>
> Updated views/tables:
>   * NAFeatureImp - modified:
>      * name from varchar2(30) to varchar2(50)
>   * RestrictionFragmentFeature - added:
>      * type_of_cut (sticky or blunt)
>   * SignalPeptideFeature - added:
>      * targetting
>   * GeneSynonym - added:
>      * is_obsolete
>
> New views/tables:
>
> A new sequence object on the top of NASequenceImp:
>   * GenomicSequence
>
> New views on the top of NAFeatureImp:
>   * ChromosomeElement
> NB : (centromere, telomere => SO)
>   * InflectionPointFeature
>   * RepeatFeature
> NB : repeat type => SO
>   * RepeatRegionFeature
>   * ReplicationFeature
>   * TransposableElementFeature
> NB: SO would give the type
>   * RNARegulatory
>   * RNASecondaryStructure
>   * SpliceSiteFeature
>
> New views on the top of AAFeatureImp:
>   * AASecondaryStructure
>   * AATertiaryStructure
>   * DomainFeature
>   * PeptideProperty
>   * PostTranslationModification
>   * TransmembraneDomainFeature
>
> A new table:
>   * PeptidePropertyType
>
>
> Note that the design takes into account the use of the Sequence 
> Ontology (SO) to refine the types of some the features, eg to 
> differentiate the different types of transposable elements, of repeats 
> or of chromosome elements (centromere, telomere ...).

Re: [Gusdev-gusdev] DNA, RNA and Protein GUS Features + PeptidePropertyType Table

[Arnaud K. <ax...@sa...>]

Hi Chris

 Chris Stoeckert wrote:

> Hi Arnaud,
> I finally went through your list. These will certainly enrich GUS! 
> Some questions/issues though.
> First a general request for documentation of the tables and attributes 
> to explain what they are to be used for. We have a plug-in that takes 
> a file in the format:
>
> TableName\t\tdescription
> TableName\tAttributeName\tDescription

Sorry for the lack of documentation, I'm going to prepare a doc file.

>
> In particular, I am curious as to what InflectionPointFeature and 
> ReplicationFeature are.

In Leishmania, but more generally for any organism which has 
polycistronic transcription, the inflection point represents the start 
of the transcription. There are some studies trying to find out whether 
or not it corresponds to a conserved sequence. If so, it might 
interesting for curator to annotate them.
ReplicationFeature represents origins of replication. ReplicationFeature 
sounds more generic but they will be given a more specific SO term.

>
> For the NAFeature views you propose, are you using "source_id" to 
> point to SRes:SequenceOntology? If so, why not call the attribute "so_id"?
> Similarly, for GenomeSequence as a view of NASequence, is this what 
> "source_id" is for?

The source_id is not related to Sequence Ontology.
The main point with my proposal is to replace controlled vocabularies 
specifying the type of a feature with SO. But to do so, I think we need 
a many to many relationship between feature views and SO. Could it be 
done by using the "DoTS::GOTermAssociation 
<http://www.cbil.upenn.edu/cgi-bin/GUS30/schemaBrowser.pl?db=GUS30&table=DoTS::GOTermAssociation&path=DoTS::GOTermAssociation>" 
table or cloning it ?
As I realise it's an important point for the GUS design, please let me 
know if you agree or  if you want to propose something else.

I added a source_id to the sequence and NAfeature views because I can 
see that all feature objects have this attribute. What is this attribute 
for in GUS ?

>
> The AAFeature views have "name" attributes and I wonder whether we 
> should have a table in SRes for controlled vocabulary terms for 
> protein features that we can point to (as with sequence ontology). 
> This would avoid the uncontrolled use of "name." I notice that 
> PeptideProperty has been given a controlled vocabulary table 
> PeptidePropertyType in this regard. Rather than have a table for each, 
> we could centralize them. Any choices for the resource to use for 
> these names? SWISS-PROT?

SO doesn't cover protein features but would eventually. Anyway in the 
meantime, it makes sense to have a controlled vocabulary. I'm not aware 
of such controlled vocabulary though.

Shall I replace the PeptidePropertyType table by a more generic one, 
AAFeatureName ?

>
> Cheers,
> Chris
>
> On Tuesday, October 8, 2002, at 09:00 AM, Arnaud Kerhornou wrote:
>
>> From: Arnaud Kerhornou <ax...@sa...>
>> Date: Tue Oct 8, 2002  9:00:32 AM US/Eastern
>> To: gusdev-gusdev <gus...@li...>, 
>> gen...@li...
>> Subject: [Gusdev-gusdev] DNA, RNA and Protein GUS Features + 
>> PeptidePropertyType Table
>>
>> Hi
>>
>> I've attached the SQL statements for new views/tables in GUS3, as 
>> well as updates of existing views/tables. It covers a new sequence 
>> object and new DNA, RNA and protein features that we would like to 
>> use. Some of them have been designed to go along Sequence Ontology 
>> classification (see below).
>>
>> Here a summary of the list of new views or tables:
>>
>> Updated views/tables:
>>   * NAFeatureImp - modified:
>>      * name from varchar2(30) to varchar2(50)
>>   * RestrictionFragmentFeature - added:
>>      * type_of_cut (sticky or blunt)
>>   * SignalPeptideFeature - added:
>>      * targetting
>>   * GeneSynonym - added:
>>      * is_obsolete
>>
>> New views/tables:
>>
>> A new sequence object on the top of NASequenceImp:
>>   * GenomicSequence
>>
>> New views on the top of NAFeatureImp:
>>   * ChromosomeElement
>> NB : (centromere, telomere => SO)
>>   * InflectionPointFeature
>>   * RepeatFeature
>> NB : repeat type => SO
>>   * RepeatRegionFeature
>>   * ReplicationFeature
>>   * TransposableElementFeature
>> NB: SO would give the type
>>   * RNARegulatory
>>   * RNASecondaryStructure
>>   * SpliceSiteFeature
>>
>> New views on the top of AAFeatureImp:
>>   * AASecondaryStructure
>>   * AATertiaryStructure
>>   * DomainFeature
>>   * PeptideProperty
>>   * PostTranslationModification
>>   * TransmembraneDomainFeature
>>
>> A new table:
>>   * PeptidePropertyType
>>
>>
>> Note that the design takes into account the use of the Sequence 
>> Ontology (SO) to refine the types of some the features, eg to 
>> differentiate the different types of transposable elements, of 
>> repeats or of chromosome elements (centromere, telomere ...).
>
>
>

Re: [Gusdev-gusdev] DNA, RNA and Protein GUS Features + PeptidePropertyType Table

[Arnaud K. <ax...@sa...>]

Chris

please find attached the documentation file. Let me know if the syntax 
is not correct.

This doc file gives information about the proposal I sent. It also 
includes some comments, following the feed-back you sent.

The proposal needs now to incorporate your feed-back, in particular 
regarding the controlled vocabulary tables.

cheers
Arnaud

Chris Stoeckert wrote:

> Hi Arnaud,
> I finally went through your list. These will certainly enrich GUS! 
> Some questions/issues though.
> First a general request for documentation of the tables and attributes 
> to explain what they are to be used for. We have a plug-in that takes 
> a file in the format:
>
> TableName\t\tdescription
> TableName\tAttributeName\tDescription
>
> In particular, I am curious as to what InflectionPointFeature and 
> ReplicationFeature are.
>
> For the NAFeature views you propose, are you using "source_id" to 
> point to SRes:SequenceOntology? If so, why not call the attribute "so_id"?
> Similarly, for GenomeSequence as a view of NASequence, is this what 
> "source_id" is for?
>
> The AAFeature views have "name" attributes and I wonder whether we 
> should have a table in SRes for controlled vocabulary terms for 
> protein features that we can point to (as with sequence ontology). 
> This would avoid the uncontrolled use of "name." I notice that 
> PeptideProperty has been given a controlled vocabulary table 
> PeptidePropertyType in this regard. Rather than have a table for each, 
> we could centralize them. Any choices for the resource to use for 
> these names? SWISS-PROT?
>
> Cheers,
> Chris
>
> On Tuesday, October 8, 2002, at 09:00 AM, Arnaud Kerhornou wrote:
>
>> From: Arnaud Kerhornou <ax...@sa...>
>> Date: Tue Oct 8, 2002  9:00:32 AM US/Eastern
>> To: gusdev-gusdev <gus...@li...>, 
>> gen...@li...
>> Subject: [Gusdev-gusdev] DNA, RNA and Protein GUS Features + 
>> PeptidePropertyType Table
>>
>> Hi
>>
>> I've attached the SQL statements for new views/tables in GUS3, as 
>> well as updates of existing views/tables. It covers a new sequence 
>> object and new DNA, RNA and protein features that we would like to 
>> use. Some of them have been designed to go along Sequence Ontology 
>> classification (see below).
>>
>> Here a summary of the list of new views or tables:
>>
>> Updated views/tables:
>>   * NAFeatureImp - modified:
>>      * name from varchar2(30) to varchar2(50)
>>   * RestrictionFragmentFeature - added:
>>      * type_of_cut (sticky or blunt)
>>   * SignalPeptideFeature - added:
>>      * targetting
>>   * GeneSynonym - added:
>>      * is_obsolete
>>
>> New views/tables:
>>
>> A new sequence object on the top of NASequenceImp:
>>   * GenomicSequence
>>
>> New views on the top of NAFeatureImp:
>>   * ChromosomeElement
>> NB : (centromere, telomere => SO)
>>   * InflectionPointFeature
>>   * RepeatFeature
>> NB : repeat type => SO
>>   * RepeatRegionFeature
>>   * ReplicationFeature
>>   * TransposableElementFeature
>> NB: SO would give the type
>>   * RNARegulatory
>>   * RNASecondaryStructure
>>   * SpliceSiteFeature
>>
>> New views on the top of AAFeatureImp:
>>   * AASecondaryStructure
>>   * AATertiaryStructure
>>   * DomainFeature
>>   * PeptideProperty
>>   * PostTranslationModification
>>   * TransmembraneDomainFeature
>>
>> A new table:
>>   * PeptidePropertyType
>>
>>
>> Note that the design takes into account the use of the Sequence 
>> Ontology (SO) to refine the types of some the features, eg to 
>> differentiate the different types of transposable elements, of 
>> repeats or of chromosome elements (centromere, telomere ...).
>
>
>