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Map all annotations to BiGG #20
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While this has been implemented during GSoC19, proper testing of the feature has not taken place yet. |
Finding a good BioModels subset is a task in itself, so this should likely be done differently. |
For species this seems to work as expected: ModelPolisher/src/test/java/edu/ucsd/sbrg/bigg/annotation/SpeciesAnnotationTest.java Lines 61 to 88 in 876bec7
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For reactions it also kind of works like expected, however there is an issue with foreign IDs that map to more than one BiGG-ID: those are discarded. ModelPolisher/src/test/java/edu/ucsd/sbrg/bigg/annotation/ReactionAnnotationTest.java Lines 21 to 78 in 62b6b21
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Running select distinct r.bigg_id as reaction_bigg_id, c.bigg_id as compartment_bigg_id, c.name as compartment_name
from reaction_matrix rm, compartmentalized_component cc, compartment c, reaction r
where rm.reaction_id in (select ome_id
from synonym
where synonym ilike '%ACETATEKIN-RXN%')
and rm.compartmentalized_component_id = cc.id
and cc.compartment_id = c.id
and rm.reaction_id = r.id;
yields
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The offending code is here: ModelPolisher/src/main/java/edu/ucsd/sbrg/db/BiGGDB.java Lines 753 to 758 in 62b6b21
Unfortunately this is somewhat deep in the stack and embedded in creative attempts at code deduplication.
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Last commit introduced a change to the reaction annotations. ModelPolisher/src/main/java/edu/ucsd/sbrg/db/BiGGDB.java Lines 725 to 738 in 8e2b3e5
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Suggested enhancement by @tpfau: Look over all present annotations and map every annotation that can be mapped to BiGG. For instance, if there is a KEGG compound annotation that compound will be assigned its corresponding BiGG
id
along with all other annotations available in BiGG. Especially since that annotation data is already present in the BiGG Models Database, this would make ModelPolisher much more useful.As long as ModelPolisher only relies on BiGG
id
s as an input this will always require manual matching of the originalid
used to BiGGid
s or assume that the model originally used BiGGid
s. It would be much better to make it database dependent.The text was updated successfully, but these errors were encountered: