PathwayCommons / factoid

A project to capture biological pathway data from academic papers
https://biofactoid.org
MIT License
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Distinctly-styled nodes, by type #682

Open maxkfranz opened 4 years ago

maxkfranz commented 4 years ago

TODO

Description

Q: What is the name of the feature?

A:

Q: What does this feature enable the user to do?

A:

Q: What information must the user provide to use the feature?

A:

Q: What are the applicable constraints, e.g. compatibility or performance?

A:

Q: How does this feature affect each class of user (persona)?

A:

Specification

Mockup

Details

maxkfranz commented 3 years ago

A chemical node should look something like this:

Screen Shot 2021-01-04 at 11 14 44 AM

A protein is usually shown as something like the following, but we should probably use something simpler:

Screen Shot 2021-01-04 at 11 17 27 AM
jvwong commented 3 years ago

FYI: https://pubs.rsc.org/en/content/articlelanding/2021/cb/d0cb00197j

d0cb00197j-f2_hi-res

maxkfranz commented 3 years ago

Yeah, the simplest version of those kind of icons would be just circles and hexagons.

Our complexes don't look like a typical figure, but there are tradeoffs re. editing

jvwong commented 3 years ago

An example of where this would help PDCD2 functions as an evolutionarily conserved chaperone dedicated for the 40S ribosomal protein uS5 (RPS2). Anne-Marie Landry-Voyer et al, Nucleic Acids Res 48 2020. Note the groundings are partially incorrect

Screen Shot 2021-09-20 at 10 50 28 AM