BEL v2.2 Enhancements

Charles Tapley Hoyt
BEL News
Published in
3 min readSep 24, 2019

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Following the Autumn 2019 meeting of the BEL Committee, the BEL v2.2 standard was finalized with the addition of following three BEPs. These updates focused on simplification of the language and encouraging standards compliance with MIRIAM and Identifiers.org.

The changes are listed below in their BEPs below:

KTSDESIGN/SCIENCE PHOTO LIBRARY/Getty

BEP-0008 — Update Namespace and Identifier Handling

BEP-0008 updates the syntax for identifiers (`<namespace>:<identifier>`) to include an optional label with the use of the `!` as inspired by OBO syntax. Now, an identifier may be defined like `<namespace>:<identifier>[!<label>]`.

For example, `p(HGNC:MAPT)`, could be optionally written using BEP-0008 syntax like `p(HGNC:6893!MAPT)`, which includes both the identifier (6893) and the label (MAPT) of the human Tau protein.

BEP-0008 also makes clear the characters that are allowed in each piece of an identifier, and when quoting are necessary. Previously, it was unclear whether lowercase letters could be used in the `<namespace>`, or which special characters were allowed. Now it is clear that uppercase letters, lowercase letters, dashes, and dots are allowed to be inclusive towards the keywords used in Identifiers.org.

BEP-0009 — Definition of Namespaces and Annotations using MIRIAM

BEP-0008 extends the syntax for defining namespaces and annotations via regular expressions (as introduced in BEP-0005 to flag the parser to look up the appropriate regular expression from MIRIAM.

This means that rather than needing to look up regular expressions in Identifiers.org by hand to write:

DEFINE NAMESPACE HGNC AS PATTERN “^((HGNC|hgnc):)?\\d{1,5}$”

The following shorthand can be used:

DEFINE NAMESPACE HGNC AS MIRIAM

BEP-0010 — Updated BEL Relationships

BEP-0010 introduces the partOf relationship to the BEL language that mirrors the relationship by the same name in the Gene Ontology and many other biomedical ontologies.It also deprecates the `subProcessOf`, `hasComponent`, and `hasComponents` relationships.

This `partOf` relationship will replace the `subProcessOf` relationship in the case of one biological process being a subprocess (part of) another biological process. The `partOf` relationship will also replace the `hasComponent` relationship that connects complexes to their members, noting that the relationship is the opposite direction.

This BEP also deprecates the `hasMember` and `hasMembers` relationships. The `isA` relationship will replace the `hasMember` relationship in the case of a protein being a member of a protein family.

The deprecated relationships `subProcessOf`, `hasComponent`, `hasComponents`, `hasMember`, and `hasMembers` will be removed in the next backwards-incompatible release of the BEL language (3.0.0+). In the mean time, all other edges can be automatically upgraded by implementations of BEL.

Credits

John Bachman, Natalie Catlett, William Hayes, and Charlie Hoyt served on the BEP committee to approve these changes.

Additional Notes

Anyone can propose BEP’s by following the instructions. If you have a change to BEL that you would like to propose and are having trouble developing the BEP, you can contact me or anyone else on the committee for assistance.

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Charles Tapley Hoyt
BEL News

Bio/chemoinformatician, software developer, open scientist