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SEP 040 -- Change BioPAX to SBO

SEP
Title Change BioPAX to SBO
Authors Jacob Beal (jakebeal@ieee.org)
Editor
Type Data Model
SBOL Version 3.0
Replaces
Status Accepted
Created 10-Jan-2020
Last modified 10-Jan-2020
Issue #88

Abstract

The Component field type is currently REQUIRED to use a BioPAX term, which is limiting and does not match with the SBO terms used on Interactions and Participations and in SBOL Visual. This SEP proposes changing to SBO, following the same mapping previously used with SBOL Visual.

Table of Contents

1. Rationale

BioPAX gives definitions for very few classes of molecular species, whereas SBO provides a much richer and more extensible set of terms. Moreover, Interations and Participations already use SBO terms. As a result, changing the type of components to recommend SBO terms rather than BioPAX terms will be both more expressive and more consistent.

In fact, SBOL Visual has already switched from BioPAX to SBO, retaining BioPAX terms as deprecated with the expectation that the SBOL data model would make the same switch with SBOL 3.0.

As such, this SEP proposes to change all BioPAX type values to their SBO equivalents.

2. Specification

Specification Changes

Table 2 BioPAX terms will be changed to replace each term with its corresponding SBO term. We also do no longer need to try to distinguish whether DNA and RNA components are the "whole" sequence or only part of the sequence, which never really made sense when considering parts designed to be composable.

Old table:

ComponentDefinition Type URI for BioPAX Term
DNA Molecule http://www.biopax.org/release/biopax-level3.owl#Dna
DNA Region http://www.biopax.org/release/biopax-level3.owl#DnaRegion
RNA Molecule http://www.biopax.org/release/biopax-level3.owl#Rna
RNA Region http://www.biopax.org/release/biopax-level3.owl#RnaRegion
Protein http://www.biopax.org/release/biopax-level3.owl#Protein
Small Molecule http://www.biopax.org/release/biopax-level3.owl#SmallMolecule
Complex http://www.biopax.org/release/biopax-level3.owl#Complex

New table:

ComponentDefinition Type URI for BioPAX Term
DNA SBO:0000251 Deoxyribonucleic acid
RNA SBO:0000250 Ribonucleic acid
Protein SBO:0000252 Polypeptide Chain
Simple Chemical SBO:0000247 Simple chemical
Complex SBO:0000253 Non-covalent complex

3. Examples

No examples are needed.

4. Backwards Compatibility

From SBOL 2 to SBOL 3, all BioPAX terms can be directly mapped onto SBO terms

Converting backward, there is ambiguity whether SBO:0000251 should map to BioPAX:Dna or BioPAX:DnaRegion (and likewise for RNA). It can likely be resolved with the heuristic that in general DNA and RNA for components should be mapped to a Region rather than a Molecule.

5. Discussion

Copyright

CC0
To the extent possible under law, SBOL developers has waived all copyright and related or neighboring rights to SEP 040. This work is published from: United States.