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Parse MetaCyc SBML file into graph database #4

Merged
merged 42 commits into from
Jan 20, 2022
Merged

Parse MetaCyc SBML file into graph database #4

merged 42 commits into from
Jan 20, 2022

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y1zhou
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@y1zhou y1zhou commented Dec 19, 2021

Extract compartments, compounds (species), reactions, and gene products from the SBML file and feed them into the neo4j database.

y1zhou added 13 commits December 14, 2021 17:57
@y1zhou
feat(metacyc): read metacyc SBML file and setup graph database
8ba4a00
@y1zhou
feat(metacyc): parse compartments and species
7a83081
@y1zhou
feat(metacyc): prepare for parsing RDFs in annotation
639e6bb
@y1zhou
fix(metacyc): arguments should be passed within lambda function
b0f2f84
@y1zhou
feat(metacyc): add RDF nodes in the Annotation section
0352323
@y1zhou
refactor(metacyc): extract function for adding RDF nodes
8656b00
@y1zhou
fix(metacyc): always use metacyc ID for consistency
009f366
@y1zhou
feat(metacyc): parse gene products and add to graph
84a58c4
@y1zhou
feat(metacyc): add reaction node basic properties and RDF links
a10f367
@y1zhou
feat(metacyc): add reactant and product links to reaction nodes
cd5a07f
@y1zhou
feat(metacyc): add associated gene products to the reactions
9d21df3 
Also update sphinx docs
@y1zhou
fix(metacyc): arg passed into add_gene_product_association_node shoul…
bb1ce55 
…dn't be GeneProductAssociation

the recursive method requires the input node to be the node that should be parsed directly
@y1zhou
fix(metacyc): normalize URI before splitting
ba4989b
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y1zhou commented Dec 19, 2021

y1zhou added 16 commits December 21, 2021 13:25
@y1zhou
feat(metacyc): prepare for parsing pathways.dat file
6750be5
@y1zhou
test(metacyc): glycolysis pathway test files
bc84361
@y1zhou
refactor(metacyc): make it clear which files should be parsed
190d5f1 
The SBML file must be given. Reaction and pathway files are optional. The corresponding functions
should read the dat files and add relevant information to the graph database.
@y1zhou
test(metacyc): reaction.dat file containing glycolysis reactions
c8d0382
@y1zhou
feat(metacyc): concatenate continuation lines in .dat files
d20348c
@y1zhou
feat(metacyc): read .dat file as key-attribute pairs
a353292
@y1zhou
feat(metacyc): extract canonical reaction ID from the full form in gr…
d6b8a53 
…aph db

fix #9
@y1zhou
feat(metacyc): parse additional information in reactions.dat
edfe1a2 
fix #8
@y1zhou
refactor(metacyc): extract function for adding link to citation nodes
662cdac
@y1zhou
refactor(metacyc): change sbml reader to staticmethod
7d5a428
@y1zhou
feat(metacyc): add pathway.dat information to Pathway node properties
af89bbf
@y1zhou
feat(metacyc): link pathway nodes to super-pathways and citations
0fd3175
@y1zhou
refactor(metacyc): extract helper functions for converting camelcase …
5721188 
…and constructing dict
@y1zhou
fix(metacyc): ensure " - " in attribute value doesn't get split
834b99e
@y1zhou
refactor(metacyc): use helper functions for adding properties to nodes
266b364
@y1zhou
fix(metacyc): use match to skip nodes that are already created
f09c811
y1zhou added 13 commits January 18, 2022 15:58
@y1zhou
feat(metacyc): parse species and taxon-range info from pathways.dat
0a1afc2
@y1zhou
fix(metacyc): avoid creating duplicated reaction nodes
0214bee
@y1zhou
feat(metacyc): links between reactions, i.e. preceding events
e4f608f
@y1zhou
fix(metacyc): change reactant/product to left/right to reflect direct…
4a37e4e 
…ion of reaction
@y1zhou
fix(metacyc): only replace dash in resource ID, not in ID value
e1531ab
@y1zhou
feat(metacyc): rate limiting step of pathways
8a6f231
@y1zhou
feat(metacyc): primary reactants and products of pathways
bead30c
@y1zhou
feat(metacyc): parse reaction layout and add primary metabolites in p…
56d813c 
…athway

The primary reactants and products are extracted from the REACTION-LAYOUT attribute, and the side is
determined by DIRECTION

fix #5
@y1zhou
feat(metacyc): parse pubs.dat and add citation annotations
e4c7339 
fix #15
@y1zhou
refactor(metacyc): use shared session for all neo4j operations
e01222f
@y1zhou
refactor(metacyc): move reaction attributes inline to be consistent w…
3eaf68b 
…ith other dat files
@y1zhou
feat(metacyc): parse classes.dat and add information on Compartment a…
ec76534 
…nd Taxa nodes

fix #13
@y1zhou
feat(metacyc): add annotation of compounds
fc7c749 
Comments in Compound nodes require parsing. DBLINKS could be added to RDF ndoes.

fix #16
y1zhou
y1zhou commented Jan 20, 2022
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A lot of new features added, with the following information still missing in the graph:

@y1zhou y1zhou merged commit 19e3426 into main Jan 20, 2022
@y1zhou y1zhou deleted the metacyc branch February 2, 2022 19:41
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