scastlara / ppaxe Goto Github PK
View Code? Open in Web Editor NEWText mining tool to retrieve protein-protein interactions from the scientific literature.
Home Page: https://compgen.bio.ub.edu/PPaxe
License: GNU General Public License v3.0
Text mining tool to retrieve protein-protein interactions from the scientific literature.
Home Page: https://compgen.bio.ub.edu/PPaxe
License: GNU General Public License v3.0
Following errors:
File "/ppaxe/bin/ppaxe", line 173, in
main()
File "/ppaxe/bin/ppaxe", line 163, in main
stats = get_ppi(options, start_time, pmids)
File "/ppaxe/bin/ppaxe", line 89, in get_ppi
query.get_articles()
File "/usr/local/lib/python2.7/dist-packages/ppaxe/core.py", line 227, in get_articles
self.__get_pubmed(req)
File "/usr/local/lib/python2.7/dist-packages/ppaxe/core.py", line 182, in __get_pubmed
article_text = minidom.parseString(req.content)
File "/usr/lib/python2.7/xml/dom/minidom.py", line 1928, in parseString
return expatbuilder.parseString(string)
File "/usr/lib/python2.7/xml/dom/expatbuilder.py", line 940, in parseString
return builder.parseString(string)
File "/usr/lib/python2.7/xml/dom/expatbuilder.py", line 223, in parseString
parser.Parse(string, True)
xml.parsers.expat.ExpatError: not well-formed (invalid token): line 34403, column 55
Error occurring on docker ppaxe.
i have down the FINAL-ner-model.AImed+MedTag+BioInfer.ser.gz, but i don't know how to use.
if can give me some idea, i'll appreciate
Scale confidence to a 0-1 value.
Add docker container to distribute ppaxe together with the StanfordCoreNLP and all the dependencies.
Right now, we only have absolute counts of each protein symbol found.
I've had a play with this and its really nice.
I'm somewhat unfamiliar with the NLP that goes into this (and NLP in general), but I wanted to know if this should be straightforward to extend to looking for interactions other than protein-protein.
For example, I'm particular interested in looking for protein-disease interactions. If I have some list of proteins and diseases I am interested in finding interactions of, do you have any advice on how I can modify the ppaxe module to do this?
Thanks!
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.