docs: updating tutorial for COMBINE25#421
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| For this dataset, two interactomes are merged (directed edges prioritized when available): | ||
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| Databases, such as STRING, contatin interactomes that represent known interacts between proteins. | ||
| - iRefIndex v13 (159,095 undirected interactions) |
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Does iRefIndex store any particular interaction like PhosphoSitePlus's kinase-substrate interactions? (We should also link to the pages.)
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I have no idea of the top of my head, but we can link the paper https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-405#Sec30.
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I believe iRefWeb, the website version of iRefIndex, is no longer available, so here are screenshots I have that I use to present the data it has:
Everything is a protein-protein interaction. The MI codes are an ontology describing those interactions.
docs/troubleshooting.rst
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| TODO: add in the errors that people could possibly run into | |||
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[We can do this in a separate PR if we want to merge this first update in first, unless we prefer bigger documentation PR updates.]
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I think this is a work in progress for now and will constantly be updated. This could be it's own pr but if I have time I will have some stuff to add to it.
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Should this be a general troubleshooting page with a subsection on Docker?
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Oh that actually would be a better page.
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We should drop this file before merging in this PR.
Co-authored-by: Anthony Gitter <[email protected]> Co-authored-by: Tristan F.-R. <[email protected]>
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Here are two final rephrasing suggestions. Then I think we should merge and use this version for Wednesday. We can continue improving it afterward.
Co-authored-by: Anthony Gitter <[email protected]>
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