Commit a07311f2 authored by Marek Ostaszewski's avatar Marek Ostaszewski
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Update Readme.md

parent 10de1775
......@@ -41,19 +41,13 @@ Results of the different tools, models and scripts are available in the correspo
* **Charles Auffray** - *Tagging publications, identification of molecular and cellular pathways and virus-host interactions, muti-organ and multi-scale modelling*
* **Augustin Luna** - *Code for aligning text-mining results with COVID19 DiseaseMaps
Automated conversion of CellDesigner COVID19 DiseaseMaps to SBGN (https://cannin.github.io/covid19-sbgn)
Code to SBGNML to annotated edgelist/tab-delimited table (example output: https://www.dropbox.com/s/pcv7xsdiff54smd/pamp.simp.tsv.txt?dl=0)
Code to convert text-mined results (using Indra: https://indra.readthedocs.io/en/latest/; compatible with Rupert Overallís results) to annotated edgelist/tab-delimited table (example output: https://www.dropbox.com/s/4i9a5wfm8rr8g2v/biorxiv.tsv.txt?dl=0); the example is from ~800 Biorxiv/Medrxiv articles from the CORD19 dataset*
* **Augustin Luna** - *Code for aligning text-mining results with COVID19 Disease Map*
* **Marina Esteban - MarÌa PeÒa - JoaquÌn Dopazo** - *AF mechanistic modelling of COVID19 Maps and integration in HiPathia tool*
* **Marina Esteban - Maria Pena - JoaquÌn Dopazo** - *AF mechanistic modelling of COVID19 Maps and integration in HiPathia tool*
* **John Bachman - Benjamin Gyori - Harvard Medical School INDRA Team** - *INDRA database: https://db.indra.bio - Unified database incorporating pathway DBs (Pathway Commons, BioGrid, etc.) and text mining results from multiple readers (REACH, Sparser, RLIMS-P, TRIPS, etc.) used to process all PubMed abstracts along with full texts from Pubmed Central and Elsevier
INDRA network search: https://network.indra.bio - Signed and unsigned search for causal paths over information in the INDRA database. Can be used to identify common regulators/inhibitors of multiple targets, identify mechanistic rationales for proposed drugs, etc.
Covid-19 knowledge network on EMMAA: https://emmaa.indra.bio/dashboard/covid19/?tab=model - Knowledge network assembled from machine reading of CORD-19 article corpus plus additional Covid-19/SARS-CoV-2 relevant papers in PubMed. Network is automatically updated with new extractions as they are published, and can be queried within EMMAAA or browsed on NDex (http://www.ndexbio.org/#/network/a8c0decc-6bbb-11ea-bfdc-0ac135e8bacf).
CLARE dialog system for Slack - Natural-language based Slack bot to build mechanistic models through interactive querying of molecular mechanisms from multiple resources including the INDRA database. Can be incorporated within the hackathon Slack workspace.*
* **John Bachman - Benjamin Gyori - Harvard Medical School INDRA Team** - *INDRA database: https://db.indra.bio - Unified database incorporating pathway DBs (Pathway Commons, BioGrid, etc.) and text mining results from multiple readers (REACH, Sparser, RLIMS-P, TRIPS, etc.) *
## Acknowledgments
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