This repo is supersceded by the RTX team repo.
The RTX Reasoning Tool POC software is being collaboratively developed by a team of investigators at Oregon State University, the Institute for Systems Biology, and Ohio State University.
codeAll software code files for the RTX proof-of-concept (POC) are accessible (and version-controlled) under this subdirectory. The RTX POC software code is 97% Python3, with the remainder being small bash scripts, Cypher queries, etc.
dataText data files for the RTX system that are deployed using git are stored under this subdirectory. There are only a few such files because the RTX POC software obtaines most of the information that makes up the biomedical knowledge graph by RESTfully querying web-based knowledge sources, rather than by loading flat files.
team-privateThis subdirectory contains notes and other documents for sharing within the RTX team.
The software that we would develop if awarded OT2 research support to build RTX would be made publicly available, under the MIT open-source software license, in the RTX GitHub area.
The RTX POC software depends on a SQLite cache file, orangeboard.sqlite. The
POC software can build this cache file if the cache file is not pre-installed by
the user; however, the POC software will build the knowledge graph much more
rapidly the first time, if our pre-built cache file (46 GB) is used. The
pre-built cache file is stored in Amazon S3
(link; requires pre-arrangement for access).
Neo4j and Python modules: please see the README file in the code subdirectory for more information.
Our team makes extensive use of the GitHub Issues system for project management. Browsing the open and (~100) closed RTX issues will provide a sense of our team's workflow and organizational style, at least for a one-month POC project.
| Name | Role | GitHub username | Areas of relevant expertise | |
|---|---|---|---|---|
| Stephen Ramsey | Project PI, Oregon State University | stephen.ramsey@oregonstate.edu |
saramsey | compbio, systems biology |
| David Koslicki | Project Co-PI, Oregon State University | dkoslicki@math.oregonstate.edu |
dkoslicki | compbio, graph algorithms |
| Eric Deutsch | PI, subaward, Institute for Systems Biology | eric.deutsch@systemsbiology.org |
edeutsch | bioinformatics, data management |
| Arnab Nandi | PI, subaward, Ohio State University | arnab@cse.ohio-state.edu |
arnabdotorg | UI for querying knowledge-bases |
| Name | Affiliation | GitHub username | Areas of relevant expertise | |
|---|---|---|---|---|
| Liang Huang | Oregon State University | liang.huang@oregonstate.edu |
lianghuang3 | natural language processing |
| Arash Termehchy | Oregon State University | arash.termehchy@oregonstate.edu |
arashtermehchy | databases, knowledge graphs |
| Theo Knijnenburg | Institute for Systems Biology | theo.knijnenburg@systemsbiology.org |
tknijnen | systems biology, Translator |
| Sui Huang MD PhD | Institute for Systems Biology | sui.huang@systemsbiology.org |
medicine, systems biology | |
| Gustavo Glusman | Institute for Systems Biology | gustavo.glusman@systemsbiology.org |
computational genomics |