standards > model/format > DOI:10.25504/FAIRsharing.Hbvvle
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ready BpForms Grammar


General Information
The BpForms Grammar extends the IUPAC/IUBMB notation commonly used to represent unmodified DNA, RNA, and proteins to describe non-canonical forms of DNA, RNA, and proteins. Features include the representation of a wider range of monomeric forms, including monomeric forms that are not described in pre-defined alphabets; left and right caps such as 5' caps; intrastrand crosslinks (additional bonds between non-adjacent monomeric forms); nicks (absence of a bond between adjacent monomeric forms); and linear and circular topologies of polymers. BpForms has concrete semantics for generating molecular structures from its compressed representation of sequences of monomeric forms. The BpForms grammar is defined in Lark syntax , which is based on EBNF syntax



How to cite this record FAIRsharing.org: BpForms Grammar; BpForms Grammar; DOI: https://doi.org/10.25504/FAIRsharing.Hbvvle; Last edited: Dec. 19, 2019, 11:07 a.m.; Last accessed: Sep 21 2020 1:14 p.m.

Publication for citation  BpForms and BcForms: Tools for concretely describing non-canonical polymers and complexes to facilitate comprehensive biochemical networks Paul F. Lang, Yassmine Chebaro, Xiaoyue Zheng, John A. P. Sekar, Bilal Shaikh, Darren A. Natale, Jonathan R. Karr; arXiv ; 2019.


This record is maintained by jonrkarr  ORCID

Record added: Nov. 5, 2019, 12:27 p.m.
Record updated: Nov. 6, 2019, 1:39 p.m. by The FAIRsharing Team.

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BpForms and BcForms: Tools for concretely describing non-canonical polymers and complexes to facilitate comprehensive biochemical networks

Paul F. Lang, Yassmine Chebaro, Xiaoyue Zheng, John A. P. Sekar, Bilal Shaikh, Darren A. Natale, Jonathan R. Karr
arXiv 2019

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Datanator
Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms.

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  • INSPIRE (National Science Foundation (NSF), USA)

  • MIRA R35 award (National Institutes of Health (NIH), Bethesda, MD, USA)

  • P41 award (National Institutes of Health (NIH), Bethesda, MD, USA)