BEL Conference 2018 - reviewing the BEL.bio API and tooling along with a quick introduction to BioDati Studio

1. BEL.bio and BioDati Studio

2. Why BEL?
Chemists have the Chemical Reaction Language
Biologists have the Biological Expression Language (BEL)
Open standard for communication and knowledge-storage
Whiteboard and Computer friendly
Partial chemical synthesis pathway: https://www.synarchive.com/syn/128

3. Overall Goals for BEL.bio
Try to simplify use of BEL and BEL Content
Stronger BEL/Nanopub validation, better error messages
Easy addition of new BEL Language features
Convert to Python and Docker
Easier community engagement
Quick easy startup/deployment
Provide API and Namespaces hosting
Easier to use/deploy/maintain search/completion service
Greatly expand organisms supported (all EntrezGene/NCBITaxonomy)
Simplify addition/maintenance of namespaces/zero downtime updates!!!

4. Glossary
BEL Assertion – single string version of BEL or subject, relation, object
(SRO) version of BEL assertion (e.g. BEL triple)
BEL Nanopub – BEL triple, Evidence, Context, Citation, Metadata
Evidence – short text extraction or supporting information for BELTriple (Evidence
in BEL Script, Support in OpenBEL Nanopub format)
Annotations – OpenBEL Annotations are now called Annotations and were referred
to as Experimental Context in BELMgr
BEL Edge – BEL triples, primary and computed BEL canonicalized to
standard namespace IDs and potentially orthologized stored in the
EdgeStore (a graph database)
API – BEL.bio API – BEL language, nanopub, terminology (namespace,
orthology) services
AST – Abstract SyntaxTree of BEL Statement
Function: BEL function, e.g. p() or modifier function, e.g. var()
NSArg: Namespace argument, e.g. HGNC:AKT1
StrArg: String argument, e.g. pmod(Ph,T, 22), Ph,T and 22 are string arguments

5. Not supported by BEL.bio
KAMs
OpenBEL API/tooling
BELScripts (except for converting to BEL Nanopubs)
XBEL
OpenBEL namespace/equivalence files (limited conversion to
BEL.bioTerminology files)

6. BEL Parsing and Validation
bel_lang python module
Depends on BEL.bio API for terminology services (namespaces, equivalents,
orthology)
Parsing, validation, canonicalization, orthologization, compute
edges (eventually completion and migration)
Uses BEL Specification and EBNF file for parsing and semantic
validation
EBNF file used byTatsu module to create parser library to parse BELTriple
into dictionary AST of Function, NSArg, StrArg components,AST is
transformed to python AST class-based object (BEL Object  BO)
BEL Spec used to process BO for semantic validation
bo.parse('p(MGI:A1bg)').orthologize('TAX:9606').canonicalize().ast.to_string(fmt='medium')
p(EG:1)
Provides CLI installed with module

7. Supports Multiple BEL versions
Can deploy bel_lang with multiple BEL versions (only BEL 2.0.0
currently (using semantic versioning now for BEL)
One BEL Specification file per version, EBNF/parser generated from
BEL Spec
Drop in new BEL Spec, get new BELVersion functionality, easy
testing of proposed BEL language features
Future: create BEL migration signatures like the computed edge
signatures for migrating BEL

8. BioDati Studio

13. Terminology Services

14. BEL Terminology Resources
Simplify Namespaces
GOBP, GOCC, GOBPID, GOCCID -> GO
Context (Annotations) are now also Namespaces
Simplify generator scripts
Single script per resource: download and reformat into
terminology or orthology load file
Single download/cache directory (gzipped)
BEL Resource tools Github repo
https://github.com/belbio/bel_resources

15. Terminology Workflow

16. Term Completion Examples – BioDati Studio

17. Namespaces Count
EG 20,750,186
TAX 1,736,298
SP 557,012
AFFX 327,392
CHEBI 106,644
MGI 57,532
RGD 44,972
GO 44,922
HGNC 41,315
ZFIN 23,388
MESH 19,223
UBERON 13,232
DO 8,699
CL 2,194
EFO 937
Terminology Statistics

18. Summary

19. BioDati Services
BioDati Studio
Data Stores (Nanopubs, Networks, Edges)
Terminologies (collection, normalization, search, completions)
Consulting – BEL-related

20. Acknowledgements
NatalieCatlett, PatientsLikeMe
Anselmo DiFabio, BioDati
David Chen
Tony Bargnesi
Nick Bargnesi

21. Additional resources
http://bel.bio
http://biodati.com
http://medium.com/biodati
JSON philosophy: https://towardsdatascience.com/my-love-affair-
with-json-edaca39e8320
https://github.com/belbio

22. location: 1501 Main Street, Rahway, NJ 07065 | call: 732-764-8844 | online: biodati.com
Anselmo Di Fabio
adifabio@biodati.com
William Hayes
whayes@biodati.com