Benjamin M. Gyori
Benjamin M. Gyori
Two comments: for most proteins we don't query the web service at all anymore. And also, for many proteins the RDF file is okay and only some error like the...
Done along the way.
Integrating xrefs between OBO-sourced IDs actually turns out to be problematic for several reasons: 1. Several xrefs point to obsolete or non-existent entries in other ontologies 2. Several xrefs are...
This is partially resolved in 995c800d1e34e594272e196cb50b3992cd1bda57 by making "INDRA json" optional but there are still some unresolved issues: - how to make this attribute hidden on the NDEx web UI?...
Well, users of INDRA would never really notice any change, it's only during internal development (of e.g., pre-assembly algorithms or input processors) that one could make a mistake by attempting...
It turns out that there is a large number of entries that neither specify an action, nor declare that there is a direct interaction between the drug and the target....
Here is a proposed signature for the new Statement: ``` Bind(agent1, agent2, agent1_site=None, agent2_site=None, agent1_site_mod=None, agent2_site_mod=None) ``` Examples: ``` Bind(BRAF, RAF1) Bind(HRAS(bound_conditions=[BoundCondition(GTP, True)]), None, "RBD") Bind(EGFR, GRB2, "tyrosine", "SH2", 'phosphorylation')...
An oldie but a goodie! I am wondering if at the time I was thinking too narrowly about `agent1_site` and `agent2_site` having to be strings. It should be possible to...
After some review, I determined that this should be done after #70 and #238.
Do you have the specific statement where this happened? I'm not sure where the statement about Transposases with a variant would come from, can't find it.