In my opinion, the specification of the subcellular localization of molecules is outside of the scope of ObjTables. ObjTables aims to provide tools for encoding (any) information into collections of tables. In particular, ObjTables provides tools for using grammars to encode complex information into individual cells in tables. I think specific recommendations for how to use such grammars for representing biochemistry is a bit outside of the scope of ObjTables.
In my opinion, such recommendations belong in a layer that builds on top of ObjTables, such as SBtab, wc-lang, or wc-kb. I think its important to separate the technology stack into layers so that most of it is applicable to related fields such as genomics and synthetic biology. The following hierarchy might make sense:
ObjTables
SBtab
SBtab-SBML
wc-lang
wc-kb
At the moment, wc-lang and wc-kb use the following conventions:
Individual species
A[c]
Reactions contained in a single compartment:
[c]: A + B ==> C + D
Reactions that span multiple compartments
A[c] + B[e] ==> C[c] + D[e]
As I've been working on the documentation, I've been thinking about what SBtab should be. I'd like to discuss this. Initially, I suggested that SBtab be a module for biology-specific data types or a specific schema for a tabular representation of SBML. However, in the context of Objtables, I think its confusing to call a specific module SBtab when the others have names such as math, sci, and chem, in part, because ObjTables doesn't really have attribute types specific to systems biology. I still think labeling a tabular schema for SBML as something like SBtab-SBML makes sense, but this is a bit different than the original SBtab schema which covers a subset of SBML and also includes schemas for data related to biochemical models.
Perhaps SBtab shouldn't be a module of attributes or a specific schema, but a set of recommendations for schemas for systems biology information. I.e., SBtab woudn't be a piece of software, but a set of recommended conventions for encoding information into ObjTables. This could include recommendations for specific resources to use.
Recommendations for representing the structures of species (SMILES for small molecules, IUPAC/FASTA for unmodified sequences, BpForms for modified sequences, BcForms for complexes)
Recommendations for encoding localization information
Recommendations for capturing references to entries in external databases (i.e. Identifiers.org)
Recommendations for specific ontologies to use to annotate information.
In my opinion, the specification of the subcellular localization of molecules is outside of the scope of ObjTables. ObjTables aims to provide tools for encoding (any) information into collections of tables. In particular, ObjTables provides tools for using grammars to encode complex information into individual cells in tables. I think specific recommendations for how to use such grammars for representing biochemistry is a bit outside of the scope of ObjTables.
In my opinion, such recommendations belong in a layer that builds on top of ObjTables, such as SBtab, wc-lang, or wc-kb. I think its important to separate the technology stack into layers so that most of it is applicable to related fields such as genomics and synthetic biology. The following hierarchy might make sense:
At the moment, wc-lang and wc-kb use the following conventions:
As I've been working on the documentation, I've been thinking about what SBtab should be. I'd like to discuss this. Initially, I suggested that SBtab be a module for biology-specific data types or a specific schema for a tabular representation of SBML. However, in the context of Objtables, I think its confusing to call a specific module SBtab when the others have names such as
math,sci, andchem, in part, because ObjTables doesn't really have attribute types specific to systems biology. I still think labeling a tabular schema for SBML as something like SBtab-SBML makes sense, but this is a bit different than the original SBtab schema which covers a subset of SBML and also includes schemas for data related to biochemical models.Perhaps SBtab shouldn't be a module of attributes or a specific schema, but a set of recommendations for schemas for systems biology information. I.e., SBtab woudn't be a piece of software, but a set of recommended conventions for encoding information into ObjTables. This could include recommendations for specific resources to use.
@liebermeister thoughts?