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Pathway Commons db and web services v11.
Due by December 1, 2018•1/1 issues closed## Goal ## Release PC2 v9 BioPAX database and web service using the latest improved cPath2 and Paxtools versions; update docs and RDF (SPARQL) endpoint; collect and analyze logs with Elasticsearch tools. ## Details ## * Remove the web app for searching pathways by keywords and displaying pathway summary pages (i.e., the /view#pw; the "pathways" app is now being developed separately); * Improve pathway data merging (perhaps, add TREMBL data to the warehouse); * Improve ID coverage (ChEBI, HGNC Symbol and UniProt Xrefs), which should improve our exporting to SIF; * Improve the full-text index, should boost graph queries' performance (by excluding intermediate id-mapping step); * Extend the Web service API: add a parameter to track/log clients (optional with reasonable default value, such as 'cpath-client' or 'cytoscape'); a parameter to include/exclude SIF types; etc. * Implement graph queries based on pre-built "All" SIF graph/model; also extend the web api to optionally run these queries instead of biopax model based ones.
Due by March 1, 2017•5/5 issues closed# Goal Create a (perhaps separate from human) PC2 instance that integrates mouse pathway data sources ( UniProt, Reactome, MouseCyc, etc.). ## Details Test and fix our output formats if needed (handle non-human gene symbols properly...)
Due by May 9, 2018# Premerge BioPAX L3 Data # ## Goal ## Download and premerge Nature PID, Nature Molecules, HumanCyc, and MouseCyc pathways. Identify validation errors and report back to the provider. There is also [a google document](https://docs.google.com/Doc?docid=0AYo7lCvbgJ1zZGNyd2M5YzVfMjFjNmRwdnRndw&hl=en#New_Report_Template) to update about the issues and progress. ## Tasks ## |ID| NAME | DESCRIPTION | ETA | OWNER | STATUS | WEEK#3 | WEEK#4 | WEEK#5 | WEEK#6 | |:--|:-----|:------------|:----|:------|:-------|:-------|:-------|:-------|:-------| |1 | NCI/Nature PID Data Premerge | Get and premerge (convert, normalize, validate, save) pathways. Identify validation errors and report back to provider. | 2.5 days | Igor | | Expected a new data release | Trying the available data again; reporting in more detail| data was updated; checking... | | |2 | UCSD Nature SIG Molecule Pages Data Premerge | Get and premerge (convert, normalize, validate, save) pathways. Identify validation errors and report back to provider. | 2.5 days | Igor | | | Modified the Fetcher (to detect biopax files w/o .owl or .xml extension in the zip archive), contacted the provider for the first time (Ashok) | | | |3 | HumanCyc Data Premerge | Get and premerge (convert, normalize, validate, save) pathways. Identify validation errors and report back to provider. | 2.5 days | Ben | | | Premerge attempted. Seven critical issues exist (see issues google document). | Suzanne Paley notified of critical issues. Waiting for response. | | |4 | MouseCyc Data Premerge | Get and premerge (convert, normalize, validate, save) pathways. Identify validation errors and report back to provider. | 2.5 days | Ben | | | Premerge has been attempted. MouseCyc data is missing pathways. Several minor issues as well (see issues google document). | Carol Bult team working on fixes. | | ## Dates ## * Start - January 13, 2010 * End - January 21, 2011
Due by January 31, 2011# Pathways web page # This project is now a separate (from cPath2) one; see https://github.com/PathwayCommons/pathways and https://github.com/mj3cheun/pathways-search A HTML5, rich web app. ## Goal ## * Provide a landing page for users browsing pathway information - human readable * Index by Google (needs nice amount of text) * Instrument pages with google analytics so we can figure out what features people are using (look at google analytics for the old page to see this as well) * Link out from Cytoscape 3 (using the Node context menu -> External Links -> Pathway Databases -> Pathway Commons - opens a browser to display resulting _find pathways by keywords_ page). ## Features ## * Pathway summary - list # molecules, processes. * Include/link a pathway page with the list of molecules (this will be indexed by google) * Highlight matched keywords in the search result (e.g., search for BRCA1). * Provider name (use standard names) ### Other ideas (to review and classify) ### * Check out PC Pathway View [GoogleDoc](https://docs.google.com/document/d/1JXDV7a4t_c0-2njX6O0nFVs2DfDDf4VxT8tFrLsxpVM/edit#) Ends: mid 2015 (e.g., after PC2 v8 release)
Due by December 31, 2016# PC2 v5 release # ## Goal ## 1. cPath2 v5.0.0 software; 1. Pathway Commons 2 v5 resource (web services and data, Human only); ## Details ## * update data sources; * add more PSI-MI data (IntAct, BIND, BIOGRID, CORUM, DIP human interactions); * count unique IP addresses (by provider, command, file, etc.; add to /log summaries); * improve the web site's style. * issue #186 (a new psimi-converter),[issue #189 (no need to force adding Controls), issue #190 (robots), issue #184 (generate "Detailed Process Data" biopax file in the downloads), etc. November 2014. Done. See [the announcement](https://groups.google.com/d/msg/pathway-commons-announcements/-C_u0dyAD6Q/ECJsWsgAP6YJ).
Due by November 30, 2014•4/4 issues closed# PC2 Release # ## Goal ## To formally and publicly release: 1. cPath2 software; 1. Pathway Commons 2 resource (web services and data archives, Human only); # Details # To make the first technical release and public announce of the cpath2 software (v4.0.0) and the new public Pathway Commons 2 (PC2) resource (v0.1, Human data only) at http://www.pathwaycommons.org/pc2/ (on cBio 'miso' server, also available via http://purl.org/pc2/ or http://purl.org/pathwaycommons/pc2/ - for resolving normalized/generated URIs), which would contain the following data sources: * Reactome (BioPAX L3, Human, v43 or v44); * NCI\_Nature Curated (the BioPAX L3 from PID, with syntax err. fixed); * HPRD (PSI-MI, v9); * HumanCyc (BioPAX L3, v16); * PANTHER Pathway (%TODO: wait for the new release/fix, reduce generics to Human-only pathways) * PhosphoSitePlus (BioPAX L3) ## Tasks ## Some of them - * issue 153 (documentation) * issue #23 * issue #39 * issue #67 * issue #77 * issue #152 ## Dates ## * Start - April 2013 * End - June, 2013 Actually, done by late Sep. 2013. Imported the latest data (e.g., Reactome v46).
Due by June 30, 2013•4/4 issues closed# Pre-release (M2) # ## Goal ## 1. fix most coding tasks, deal with version numbers (decide and show in readmes and xml current versions of the code, loaded data, service configuration/db/instance) 1. develop a secure web application admin module to be used for creating and monitoring a cpath2 instance. An admin web app will help prepare data for the release and run all the cpath2 import pipeline tasks currently run via cpath-admin jar, such as configure db connections and create schemas, define metadata, fetch pathway and warehouse data (upload to the right place), run premerge, merge, indexing, etc. stages; also, - start/stop the main instance, view logs, usage summary, etc. # Details # ## Tasks ## * issue #77 * issue #78 * issue #64 ## Comments ## Will finish the Admin web app later, in the other milestone/sprint (see now it's ~20% done; issue #148 is updated) ## Dates ## * Start - March 2013 * End - April, 2013
Due by April 30, 2013•2/2 issues closed# Gene Symbols Support and ID-Mapping # ## Goal ## Make cPath2 graph query web service "understand" gene symbols in user queries and return a reasonable (best guess) sub-network (i.e., one will use official gene symbols as values for the 'source' and/or 'target' query parameters, along with full URIs, as it's currently. This is also one of goals stated in the Pathway Commons grant (thus - a requirement). Although one can get much from the current system, this work will also make things easier for most users (in most cases, they would probably have to first use our powerful "/search" query, i.e., at by least using datasource/organism/type filters, and perhaps even Lucene syntax, to find good top hits to be used as sources or targets in following "/graph" or "/get" queries...) Currently, users can either guess URIs (prone to errors, risks, incomplete data coverage) or - combine of two "atomic" cPath2 web services (flexible but does not **get the most out of the BioPAX data in hands and beyond**): a) a full-text search by gene names, source, organism, BioPAX type (very powerful and confusing; also original pathway data do not 100% guarantee one finds a protein/gene by name); then b) analyze the search results to extract relevant URIs from (all or some of) search hits to run a graph query. So, currently, our users utilize more freedom which comes with more responsibility (whereas we have less of it) for their results. Adding this new feature means doing more analysis, data post-processing, taking responsibility by our team (for introducing new/inferred relationships), but most of users should be satisfied and find it very convenient and useful. This includes and requires several decisions to be made regarding to what kind of id-mapping technology/tables to use and to what extend (hopefully, quite minimalistic and very specific) and pathway data post-processing (e.g., infer and auto-generate more Xrefs based on existing BioPAX data). We hope this Sprint can also improve merging of data (due to in-parallel improving and updating the biopax-validator, normalizer, and also that the id-mapping and newly generated Xrefs will increase chances for a not-so-well-defined original protein/chemical reference to match/merge with canonical uniprot/chebi one, and for a web service query to hit a previously missed molecules or a sub-network of interest in our database) ## Tasks ## * Issues: issue #150, issue #151, issue #152 * Test and Review ## Dates ## * Start - December 2012 * End - January-February, 2013
Due by February 14, 2013•3/3 issues closed# Switch to identifiers.org URIs and xml:base # ## Goal ## Modify cpath2 and the BioPAX validator/normalizer to generate/normalize-to standard identifiers.org URIs (but it's not for Xrefs, except for PublicationXref, types), where possible; also use own (configured) xml:base to consistently generate resolvable (URL) URIs for Xrefs. Stop encoding information and imposing a particular style into xref URIs (i.e., don't make urn:biopax:RelationshipXref:... things) ## Tasks ## | ID | NAME | DESCRIPTION | Estimated time | OWNER | | |:--|:-----|:------------|:---------------------------------------------------|:------|:--| | 1 | identifiers.org | update the biopax-validator and cpath2 (import pipeline and services) | 3 weeks | Igor | Done | | 2 | xml:base| update the biopax-validator, and cpath2 (respect xml:base) | 2 weeks | Igor | Done | | 3 | uniprot isoforms | ACs like P04150-3 are now valid IDs in the uniprot.isoform MIRIAM/identifiers.org namespace; make changes that appreciate this (in the validator); but keep merging (modify the cpath2 Merger) isoform PRs into corr. canonical one (P04150) | 1 week | Igor | Done | Done. ## Dates ## * Start - November 2012 * End - December, 2012
Due by December 31, 2012# Output Formats Improvement # ## Goal ## Fix our GSEA (.gmt) output and add SBGN to the list. ## Tasks ## | name | description | owner | time | status | |:---|:--------|:---------|:-------|:---------| | fix GSEA | split by species, make the first column unique | Igor | 1 week | complete | | add SBGN | utilize paxtools sbgn-converter; plug into the system | Igor/Osgun | 1 week | complete | Done (November 2012).
Due by November 30, 2012# Graph and Traversal Queries # ## Tasks ## | name | owner | time | status | |:--------|:---------|:-------|:---------| | "/traverse" web service | Igor/Ben | 1 week | complete | | "/graph" web service | Igor/Ben/Osgun | 1 week | complete | Done (2012).
Due by December 21, 2012# Batch Downloads # ## Goal ## Provide snapshot/batch downloads of all cpath2 data. ## Tasks ## | ID | NAME | DESCRIPTION | Estimated time | OWNER | by WEEK# 37 | WEEK#37 | WEEK#38 | |:--|:-----|:---------|:---------------|:------|:-------------|:---------|:--------| | 1 | Batch Download Service | add exporter module and downloads page...| 1 weeks | Igor | | done | | | 2 | Create Downloads pipeline | add cpath2 admin command | 1 weeks | Igor | some refactoring and bug fixing (web app, converters) | merged cpath-service commands to cpath-admin.jar/.sh; fixed maven assembly configuration. | done | | 1 | Test/Review | Fully test the batch download | TBD | TBD | | | | ## Dates ## * Start - September 10, 2012 * End - September 24, 2012
Due by September 24, 2012# Run the Webservice # ## Goal ## Have a web page like (or exactly as) http://www.pathwaycommons.org/pc/webservice.do?cmd=help - web service description with clickable examples. (**May 2, 2011: After some discussions, we've decided in this phase to support the cbio-portal use case: take a set of one or more gene symbols and returning a network of interested.)** The web service will consist of search, get, and graph commands. The search command accepts free text and returns a list of relevant RDF IDs. The get command accepts a RDF ID and returns the record in a variety of formats. The graph command accepts one or more id's and returns a graph based on the desired query. All commands accept various parameters which affect its behavior. See [this wiki page about](https://github.com/PathwayCommons/cpath2/wiki/cPathSquaredWebService) the web service design details. ## Tasks ## | ID | NAME | DESCRIPTION | ETA | OWNER | STATUS | WEEK#21 | WEEK#22 | |:--|:-----|:------------|:----|:------|:--------|:---------|:-------| | 1 | SIFNX Converter | Add ability to query interaction attributes | | Emek | done - with inverse and union accessors | | 2 | Graph Queries | Connect graph queries to cpath-service | | Ozgun | done | | 3 | Output Format | Connect GSEA, BINARY-SIF, EXTENDED BINARY-SIF (SIFNX) converters to cpath-service | 1 day | Benjamin | Complete | | 4 |Query Utils| Add "non-atomic" instruction for traversing from xrefs to entities | | Emek | Postponed - not needed for this sprint| | 5 | Filtering | Add support to filter search results by data source, organism, and BioPAX class type to cpath-service, cpath-web-service (may require changes in paxtools-core) | | Igor | done | | 6 | Help Page (prototype)| Improve the "/help" command. Create a web page that describes the web service | 1 week | Igor | done | | 7 | Web Service Page | Create a web page which describes the web service and provides example URLs | 1 week | Benjamin | Complete | | 8 | Populate database | Import UniProt, !ChEBI, Reactome (Hs) and NCI data into production database | | Igor | re-importing | done (with errors, but usable) | re-importing all; making a full-export (for testing) and validation feedback | | 9 | Testing | Test correctness of select web service calls e.g. graph | | Ethan| | | 10 | Testing | Create public testing server (e.g. on miso) | | Ben| | | 11 | Testing | Test completeness and correctness of data. Revisit BMP signaling pathway merge | | Emek, Ozgun & Gary | | ## Dates ## End - June-July, 2011 [Here is a dashboard](https://spreadsheets.google.com/spreadsheet/ccc?key=0Ag6KD6MljCkYdERKa1lkd1RZUnRGNFd3ZmtNVDNRS3c&hl=en_US), another view on the same Sprint's tasks.
Due by July 17, 2011# Import Reactome and NCI_Nature Curated (PID) Data # ## Goal ## Exercise the cpath2 import pipeline (fetching, normalizing, validating, merging) with the entire ChEBI dataset, a subset of UniProt (human, rodent, fungi) and PubChem, and two real pathway data sets (Reactome & Nature PID). ## Tasks ## | ID | NAME | DESCRIPTION | Est. time | OWNER | STATUS | WEEK#41 | WEEK#42 | WEEK#43 | WEEK#44 | WEEK#45 | WEEK#46 | WEEK#47 | WEEK#48 | WEEK#49 | WEEK#50 | WEEK#51 | WEEK#52 | WEEK#53 | WEEK#2 | WEEK#3 | WEEK#4 | |:--|:------|--------------|:------|:------|:------|:------|:------|:------|:------|:------|:------|:------|:------|:------|:------|:------|:------|:------|:------|:------|:------| | 1 | Configuring CPath2 | Setting the home directory, environment, logging, metadata, etc. on miso-dev server; java library versions; etc. | | Igor/Ben | Complete | | | | | | | Persisting larger data: Segmentation Fault (on miso-dev) and "Invalid access of stack red zone" (MacPro) - looks, we have to tune JVM and hardware parameters (-Xmx, -XX:MaxPermSize, etc., **ulimit**...) | done (per user, me): server 'ulimits' increased, JVM tuned (in the [cpath-admin.sh script](http://code.google.com/p/pathway-commons/source/browse/cpath2-mvn/distribution/src/main/etc/bin/cpath-admin.sh)), project upgraded: Spring 3.0.5, Hibernate 3.6 ([in the pom.xml](http://code.google.com/p/pathway-commons/source/browse/cpath2-mvn/pom.xml)) | | | -Xss16384k helped (on miso-dev) | | -Xss65536k helped | | | |2 | Warehouse Data Import| fetch, convert, save, index protein and small molecule reference data. | 2 weeks | Igor/Ben | Complete | now converting PubChem (so far ~6,100K SMRs, 210 of 1877 files) | restarted (continues); so far ~11,384K SMRs, ~400 of 1877 files | ~16,667,939 SMRs, ~539 of 1877 files | implement import on-demand or/and use id-mapping... (so far ~21,250,000 SMRs, 692 of 1877 files) | will stop it | stopped (at ~50% done); implemented batch re-build of lucene indexes; set default indexing to 'manual' | Ben to start refactoring of SM import/conversion based on Nov 16 discussion. See: [SM Refactoring](http://https://docs.google.com/document/d/12P88M6KAIxgT4nR-bcGQpavupwkKUaqPy9qq9QOoa-I/edit?authkey=CLzl8VI&hl=en#) | Refactoring complete. TODO: import entire ChEBI again | | done | | | | data re-imported; batch full-text indexing fails ("too many connections")?.. | (Re-)indexing - fixed! | |3 | Reactome Data Premerge| Get and premerge (convert, normalize, validate, save) Reactome pathways (human, mouse, rat, yeast). Identify validation errors and report back to provider. | 1 week | Igor/Ben | Complete | BioPAX errors and data format issues | resolving Reactome issues (Reactome L3 has been updated) | Resolving PID issues...; tuning auto-fix and normalization (new features in the validator!) | Trying new Reactome data and PID ([Issues](https://docs.google.com/Doc?docid=0AYo7lCvbgJ1zZGNyd2M5YzVfMjFjNmRwdnRndw&hl=en)). Implemented auto-fix and normalization in the Validator | several bugs fixed (in ORM, NPE, UTF-8, etc.); | a new ORM bug discovered (in paxtools/hibernate); required creating a special test data; found, fixed! | fixing, importing data... | pre-merge failure: PID has critical BioPAX errors ([Jeff is working to fix](https://docs.google.com/Doc?docid=0AYo7lCvbgJ1zZGNyd2M5YzVfMjFjNmRwdnRndw&hl=en)); [Reactome](https://docs.google.com/Doc?docid=0AYo7lCvbgJ1zZGNyd2M5YzVfMjFjNmRwdnRndw&hl=en) (Homo sapiens) crashes (Segmentation Fault or illegal stack red zone access); so far, could not find the exact reason. PantherDb has serious issues... | experimenting, debugging... | Ben takes over debugging segfault | SEGFAULTt on miso-dev resolved; Subsequent java.sql exceptions resolved. Now able to import Reactome Homo sapiens file. Will attempt to import other Reactome files next week. | Problems importing other Reactome owl files. Custom Reactome cleaner is being coded to address issues. Also addressing cross-species RDFId conflicts. | Successfully importing Reactome human, mouse, rat, yeast files. Currently repopulating SM, Protein warehouses. This will be followed by merging of Reactome data. | Reactome data merging complete. Improved cpath-admin commands | | | 4 | Pathway Data Import| Merge, Reactome and NCI\_NATURE (PID) pathways. Note: Premerging of NCI\_Nature (PID) has been moved to sprint 1b. | 1 week | Igor/Ben | | | | | | | | | | | | | | | | | | 5 | Create integration test case | Create BioPAX Level 3 files of the BMP signaling pathway [from Reactome](http://www.reactome.org/entitylevelview/PathwayBrowser.html#DB=test_reactome_34_pathway_diagram&FOCUS_SPECIES_ID=48887&FOCUS_PATHWAY_ID=201451&ID=201451), [from PID](http://pid.nci.nih.gov/search/pathway_landing.shtml?pathway_id=bmppathway&pathway_name=BMP%20receptor%20signaling&source=NCI-Nature%20curated&what=graphic&jpg=on&ppage=1), and from the cpath2 merge. Output: 3 BioPAX files, one containing each version of the pathway. | 3 days | Igor | | | | | | | | A console command to export the original, premerged, and merged owl data (for given provider / file); modify the cpath-service and also add a paxtools (console) command to extract a biopax element as a sub-model (- to owl) given its rdf id... | 99% done (waiting for the data...); **commands:** _**-fetch** (a PC sub-model by IDs), **-export-premerge** (per provider, file), **-export-pathway** (provider's orig.), **-export-validation**_ | | | | | Single '-export' command is to replace those previously added; new '--fetch' (a sub-model) command in the paxtools; extracted human BMP sig. pw. from the original and premerge Reactome. NCI does not have this pathway! | files are on miso-dev:/data/cpath2\_home/sprint1\_testdata/ | | | 6 | Test/Review | Fully test the integration test case. Load BioPAX documents into Protege and manually examine and compare to the integrated version. Also, create chibe diagrams of each of these for manual comparison. | TBD | Nadia, Arthur, Emek, Gary, Ozgun | | | | | | | | | waiting for data... | | | | | | | | ## Dates ## * Start - September 13, 2010 * End - January 2011
Due by January 31, 2011## Goal ## 1. cPath2 v6.0.0 software (store/index the BioPAX model not using H2/Hibernate db); 1. **PC2 v6 release** (web services and data, Human only); 1. PC Downloads and [Archives](http://www.pathwaycommons.org/archives/). ## Details ## * update all warehouse and pathway data sources; * issue #191 (our GSEA .gmt format); * issue #192 (URI clash in PANTHER data); * issue #180 (Downloads/Archives links - main PC web site); * issue #182 (report the approx. sub-network size); * [test](http://pathwaycommons.baderlab.org); * update the Virtuoso [SPARQL](http://rdf.pathwaycommons.org/sparql/), [FCT](http://rdf.pathwaycommons.org/fct/) (load new BioPAX RDF/XML graph into the quad store); * archive and replace PC2 v5 on the production server; * update PURLs; * announce.
Due by December 24, 2014•4/4 issues closed## Goal ## Convert and import more pathway data into PC2. ## Details ## * list and prioritize new pathway data sources. * build and run a cPath2 instance using all previous and selected new data sources. * decide on which data to include into next PC2 release. * [promised](https://drive.google.com/file/d/0B4o7lCvbgJ1zd0lCY2dDSzc4UnpXMl9HRVR6TEVIbHFack9F/view?usp=sharing) (see the 1st year); * [Arman's list](https://docs.google.com/spreadsheets/d/1Vs-LNlE6mjhwtzNfeSvn7KBqbofSkzKWYs_KflN00m4/edit?usp=sharing) (GSoC projects), plus translated KEGG hsa`*` files; * fix BIND organism issue, if possible in the original data; * create one ticket per data source on the issue tracker; * convince data providers to release the BioPAX data officially (we'd share our code, consult, etc.; update: we've already added about the benefits of exporting BioPAX for data providers to [our F.A.Q.](http://pathwaycommons.org/#faq)); We've got the following (all - human data only): 1. CTD, 1. RECON 2, 1. Small Molecule Pathway Database, 1. miRTarBase, 1. DrugBank, 1. Navicell, 1. IntAct Complex (human data are already in PC2 v5, v6; there is a special option in the new psimi-converter to generate Complexes instead of MIs), 1. MSigDB (in fact only TRANSFAC) 1. We'd also try KEGG (converted to BioPAX by Andreas D., Clemens W., BioModels), 1. PharmGKB? 1. SPIKE? Communicate with providers of selected data to figure out how data distribution and maintenance will work. See: "What are the benefits of exporting BioPAX formatted data for data providers?" question in our FAQ at http://www.pathwaycommons.org/about/ See [the PC2 v7 test instance](http://pathwaycommons.baderlab.org/) (mid December 2014). This includes, in addition to PC2 v6 data, the following: CTD, RECON X, miRTarBase, DrugBank, MSigDB (TRANSFAC), KEGG (human `*.hsa` files).
Due by January 29, 2015## Goal: ## Create PC2 v7 release. ## Tasks ## * communicate with [data providers](https://docs.google.com/document/d/1MN8D44WX-Je6SQXvAtYf-Dg6H-cjQzBLh3fsX2_QIIk/edit?usp=sharing); * Confirm data sources for inclusion (all human-only; _confirmed on Jan.13.2015_): 1. updated PC2 v6 data sources, 1. CTD, 1. RECON 2, 1. miRTarBase, 1. DrugBank, 1. MSigDB (TRANSFAC) 1. KEGG (`*.hsa` files converted to BioPAX). * resolve the Sprint14 issues * use the latest TRANSFAC BioPAX data (done); * re-build; * test, test again; * release * public announcement (Data sources confirmed, Jan.13.2015)
Due by March 1, 2015•4/4 issues closedTo release cPath2 v6.1.0; build new PC2 v8 database and update www.pathwaycommons.org/pc2/, release announcement, docs, and RDF endpoints. ## Goal ## Have more pathway data sources and less errors in PC2. Release PC2v8. ## Details ## * List and prioritize new pathway data sources (optionally: contact data providers). * Implement data mappers/converters. * Build and run a cPath2 instance using all previous and new data sources. * [promised](https://drive.google.com/file/d/0B4o7lCvbgJ1zd0lCY2dDSzc4UnpXMl9HRVR6TEVIbHFack9F/view?usp=sharing) (see the 1st year); Having done PC2 v7, we've got the following ToDo list (use human data only): 1. Small Molecule Pathway Database, 1. Navicell, 1. PharmGKB, 1. SPIKE?, 1. INOH 1. Wikipathways 1. Netpath 1. Sabio-rk 1. Biomodels 1. http://signalink.org/download 1. Rhea Which ones do we want most urgently? 1. PharmGKB (Augustin) 1. Small Molecule Pathway Database (Augustin) Which ones are easiest? (need to evaluate, but probably Rhea, Biomodels, sabio-rk) Which ones are most useful for our users? SPIKE - very complementary with existing pathway databases Which sources have been selected? * Igor will try INOH and Netpath BioPAX L3 (to validate, implement a Cleaner); * Augustin will try a couple of more sources... * at the last moment, we also included WikiPathways
Due by March 11, 2016•16/16 issues closed