Annotation package workshop 2010

19–21 May 2010

The purpose of this meeting is to work on defining a package for SBML Level 3 which supports more elaborate (full RDF) annotations, as well as defining any other types of annotation not mandatory in the Level 3 core.

Meeting organization

Neil Swainston, Dagmar Waltemath and Allyson Lister are organising the meeting, with Nicolas Le Novère hosting and providing the location and infrastructure for the physical meeting. Attendees will be distributed across at least two sites (EBI/Hinxton and University of Rostock), and videoconferencing will be used. The actual number of groups involved is larger, but some of the group representatives will travel to one of the main sites to reduce the number of connections and increase local interactions and discussions. See the table below for a list of the attendees and where they were joining from.

The organisers of each hub are responsible for organising the travel and accommodation arrangements for that hub.

Audio-visual connection information

The lead sites were the EBI near Cambridge, UK, and Rostock, Germany (contact: Dagmar Waltemath). We used a combination of systems for remote connections: a Tandberg videoconferencing system link between the EBI and Rostock (at IP address 193.62.197.99) and EVO. See the separate page of instructions for information about how to get started with EVO. The session password is "SBML" (without the double quotes).

Detailed discussion topics

On the morning of the first day, we began with a more detailed list of possible topics constructed from everyone's input prior to the meeting, then developed the following condensed list of specific topics. We also assigned "owners" to indicate the lead groups or persons to take the first pass at discussing each topic.

There is currently also a page of general notes that is being modified dynamically and will probably be emptied by the end of the workshop.

Topics discussed in addition to those below included the following:

• Format: How should the annotation package be integrated into SBML LV3 core annotation style and the "free annotation" style with arbitrary RDF?

Agenda

From the originally proposed list of topics for discussion we have put up the following programme. A detailed description of all addressed discussion points follows further down. If you have any other topics you wish to add, just email Allyson, Neil or Dagmar.

Wednesday, 19 May 2010

Thursday, 20 May 2010

Friday, 21 May 2010

Pre-meeting Background Information

The following is background reading material for the meeting.

• The discussion topics list for this workshop.

• SBML Level 3 Version 1 Specification, especially Sections 5 and 6, which concern various types of annotation.

• How to write an SBML package specification

• You should be familiar with the W3C RDF Standard

• We may bring RDFa into the discussion if appropriate. You can find more information on RDFa in the W3C RDFa Primer

Participants

Participants marked in bold are organisers of the workshop.

Attendance is by invitation from the organisers only.

Post Meeting discussion points

Annotating non-existence of entities

The annotation package provides a mean to express that a particular entity (be it a species, a reaction, a parameter, a compartment etc) is consciously not encoded in a model because we know that it must not be part of the model.

This knowledge is different to the non-conscious absence of an entity, for example, because it was just not thought about in the context of a model.

Example

biologists?

To express absence of a particular entity we introduce the listOfAbsentEntities element. It contains a number of entity definitions (annot:omittedEntities). Each of them gets a metaID assigned. Through that metaID, each of the ommitted entities can have a number of annotations assigned, following the rules of the annotation package.

The absent entities are encoded as follows:

 <annotation>
  <annot:listOfAbsentEntitities>
   <annot:omittedEntity metaid="metaidX"/>
   <annot:omittedEntity metaid="metaidY" />
  </annot:listOfAbsentEntitites>
 </annotation>

The sole name (metaid) of an omitted entity does not hold any reliable semantics with information about that entity. That is why the <rdf:RDF> description block annotates the omitted entities and only then we can infer knowledge about the biological entity that must not occur inside the model:

<annotation> 
 <rdf:RDF>
   <rdf:description rdf:about="metaidX">
    <bqbiol:is>
     <rdf:Bag>
      <rdf:li rdf:resource="urn:miriam:obo.go:GO%3A11111111"/>
     </rdf:Bag>
    </bqbiol:is>
   </rdf:description>
   <rdf:description rdf:about="metaidY">
   [..]
   </rdf:description>
  </rdf:RDF>
</annotation>

An example for the definition of two absent species is given in the following code snippet:

<listOfSpecies>
 <annotation>
  <annot:listOfAbsentEntitities>
   <annot:omittedEntity metaid="foo"/>
   <annot:omittedEntity metaid="bar" />
  </annot:listOfAbsentEntitites>
  <rdf:RDF>
   <rdf:description rdf:about="foo">
    <bqbiol:is>
     <rdf:Bag>
      <rdf:li rdf:resource="urn:miriam:obo.go:GO%3A11111111"/>
     </rdf:Bag>
    </bqbiol:is>
   </rdf:description>
   <rdf:description rdf:about="bar">
   [..]
   </rdf:description>
  </rdf:RDF>
 </annotation>
</listOfSpecies>

In the above example two omitted entities foo and bar are defined inside the listOfAbsentEntities. As the list is nested inside the SBML listOfSpecies we can infer that the absent entities foo and bar are both representing absent species. The rdf description links the absent species foo to the MIRIAM URI urn:miriam:obo.go:GO%3A11111111, using the bioqualifier is. The meaning of that annotation is: Inside the model there must not occur a species that is urn:miriam:obo.go:GO%3A11111111.

Draft proposal

Meeting discussions resulted in a draft proposal for an annot package for SBML L3.