August 2012 This work is licensed under the Creative Commons Attribution 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by/3.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA. BEL Framework Resources (namespaces, equivalences, documents) 1
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August 2012
This work is licensed under the Creative Commons Attribution 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by/3.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA.
• The BEL Framework accesses files during compilation– For checking and equivalencing namespace values– For augmenting the KAM to increase connectivity
• A set of resource files are maintained by Open BEL• Flexible - can be substituted or augmented with user
• Values with the same UUID are equivalenced– Terms containing same functions are coalesced to a single node during
compilation• Values in a namespace file are not required to be included in the
associated equivalence file
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Example: Equivalences for MGI namespace
Examples of BEL Equivalencing
• The following three protein abundance terms are equivalent:– p(HGNC:AKT1)
• The abundance of the protein designated by HUGO gene symbol ‘AKT1’
– p(EGID:207)• The abundance of the protein designated by EntrezGene Id 207
(AKT1 Human)– p(SPAC:P31749)
• The abundance of the protein designated by SwissProt Id P31749 (AKT1 Human)
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Examples of BEL Equivalencing
• The following two biological process terms are equivalent:– bp(MESHPP:apoptosis)
• The biological process designated by the MESH Phenomena and Processes heading ‘apoptosis’
– bp(GOID:0006915) • The biological process designated by the GO Id 0006915 (apoptotic
process)
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BEL Annotations
• BEL Annotations and BEL Terms are completely separate• Annotations are associated with BEL Statements to express context
information about the statement– Source of the knowledge
• Citation, Evidence – Biological system
• Cell line, Body part, Species
• 22 Annotation Types are provided with the BEL Framework – 2 reserved types: Citation and Evidence– 20 additional defined by .belanno documents
• Additional Annotation Types can be defined by user– Require unique name within BEL document and domain of allowable values
(as list or .belanno document) or regular expression
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Annotations Can Be Applied to Individual BEL Statements or Groups of Statements
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Causal relationships demonstrated in lung fibroblasts, reported in PMID 1234567
Causal relationship demonstrated in liver endothelial cells , reported in PMID 1234567
Each Statement is distinct: These Statements have different sets of contexts
Source: PMID 1234567
Cell Type: Fibroblast
Cell Type: Endothelial Cell
Tissue: Lung
Tissue: Liver
p(X) increases r(Y);
kin(p(X)) increases p(Z);
p(X) increases r(Y);
Citation Annotation Format
• The Citation annotation is composed of a comma separated list containing up to 6 fields.– SET Citation = {"PubMed","Cell","16962653","2006-10-07","Jacinto E|
Field Required Contents1 Yes Type of Citation. This is one of the following strings “Book”,
“PubMed”, “Journal”, “Online Reference”, or “Other”2 Yes Name of the Citation. This is typically the journal reference or
book name.3 Yes Reference. This is an identifier that can be used to link to the
citation. For books this is usually the ISBN number, for PubMeds this would be the PubMed ID and for other types it could be a URL pointing to the reference such as Wikipedia page.
4 No Date of publication in ISO8061 format (YYYY-MM-DD).5 No Authors. This is a “|” delimited list of authors for the reference.6 No Comments. This is optional information such as an abstract
that can be stored along with the reference. Limit is 4000 characters.
BEL Resource Documents
• BEL Resource Documents are used in compilation Phase III for network augmentation – BEL documents– Relevant assertions are identified and added to the network
• Allows use of a vocabulary not specifically supported by the BEL Framework– Including equivalencing to other namespaces
• Detailed directions can be found here:– http://openbel-framework.readthedocs.org/en/latest/tutorials/building_custom_namespaces.html
• Requires:– Namespace file in .belns format– URL for the .belns file– Customized resource index– Updated BEL Framework configuration file pointing to new resource index