Rephetio: Repurposing drugs on a hetnet

Daniel Himmelstein, Antoine Lizee, Chrissy Hessler, Leo Brueggeman, Sabrina Chen, Dexter Hadley, Ari Green, Pouya Khankhanian, Sergio Baranzini

Discussion

Subject Last comment Time Views Status
27
 How should we construct a catalog of drug indications? Daniel Himmelstein July 8, 2017 900 Completed
3
 Assessing the effectiveness of our hetnet permutations Daniel Himmelstein July 8, 2017 78 Completed
3
 Hosting Hetionet in the cloud: creating a public Neo4j instance Daniel Himmelstein May 17, 2017 292
15
 Tracking project reuse, citation, and publicity Daniel Himmelstein May 2, 2017 213 Open
9
 Using the neo4j graph database for hetnets Daniel Himmelstein April 27, 2017 657 In Progress
46
 Report Review: Rephetio: Repurposing drugs on a hetnet Daniel Himmelstein April 10, 2017 139
6
 Our hetnet edge prediction methodology: the modeling framework for Project Rephetio Daniel Himmelstein March 13, 2017 126 Open
5
 Measuring user contribution and content creation Daniel Himmelstein Feb. 8, 2017 87 In Progress
6
 One network to rule them all Daniel Himmelstein Feb. 4, 2017 324 Completed
16
 Integrating resources with disparate licensing into an open network Daniel Himmelstein Feb. 2, 2017 518 In Progress
3
 Why we predicted ictogenic tricyclic compounds treat epilepsy? Daniel Himmelstein March 10, 2017 32
14
 Visualizing the top epilepsy predictions in Cytoscape Daniel Himmelstein Jan. 31, 2017 95
13
 Using Entrez Gene as our gene vocabulary Daniel Himmelstein Jan. 26, 2017 267 Completed
14
 Brainstorming future directions for Hetionet Alex Ratner Jan. 18, 2017 155 Open
11
 Prediction in epilepsy Daniel Himmelstein Jan. 10, 2017 133
3
 Decomposing predictions into their network support Daniel Himmelstein Dec. 23, 2016 31
3
 Decomposing the DWPC to assess intermediate node or edge contributions Daniel Himmelstein Dec. 23, 2016 23
29
 Incorporating DrugCentral data in our network Mike Gilson Dec. 7, 2016 175 Completed
11
 STARGEO: expression signatures for disease using crowdsourced GEO annotation Daniel Himmelstein Nov. 30, 2016 359 Completed
4
 Evaluation framework Daniel Himmelstein Nov. 25, 2016 77 Open
7
 Mining knowledge from MEDLINE articles and their indexed MeSH terms Daniel Himmelstein Nov. 20, 2016 282 Completed
5
 Assessing the informativeness of features Daniel Himmelstein Nov. 4, 2016 114 Open
9
 Describing Hetionet v1.0 through visualization and statistics Casey Greene Oct. 18, 2016 225 Open
17
 Predictions of whether a compound treats a disease Pouya Khankhanian Oct. 16, 2016 331 Open
9
 Unifying disease vocabularies Daniel Himmelstein Sept. 22, 2016 314 Completed
6
 Exploring the power of Hetionet: a Cypher query depot Daniel Himmelstein Aug. 31, 2016 162
5
 Disease Ontology feature requests Daniel Himmelstein Aug. 10, 2016 145 Completed
11
 Sounding the alarm on DrugBank’s new license and terms of use Daniel Himmelstein June 24, 2016 553 Completed
1
 Edge dropout contamination in hetnet edge prediction Daniel Himmelstein May 16, 2016 38
2
 Introducing the Residual Degree Weighted Path Count (R-DWPC) Daniel Himmelstein May 16, 2016 68
2
 Cataloging drug–disease therapies in the ClinicalTrials.gov database Daniel Himmelstein May 8, 2016 122 Completed
5
 Computing standardized logistic regression coefficients Antoine Lizee May 2, 2016 1621 Open
8
 Data nomenclature: naming and abbreviating our network types Daniel Himmelstein April 18, 2016 165 Completed
8
 Suggestions for additional information types? Daniel Himmelstein April 16, 2016 166 Open
6
 Transforming DWPCs for hetnet edge prediction Daniel Himmelstein April 16, 2016 76 In Progress
8
 Estimating the complexity of hetnet traversal Daniel Himmelstein April 16, 2016 73 Completed
2
 Network Edge Prediction: Estimating the prior Daniel Himmelstein April 15, 2016 79 In Progress
4
 Network Edge Prediction: how to deal with self-testing Daniel Himmelstein April 14, 2016 81 In Progress
11
 Creating a catalog of protein interactions Daniel Himmelstein April 11, 2016 183 Completed
8
 Calculating genomic windows for GWAS lead SNPs Greg Way April 8, 2016 704 Deferred
3
 MSigDB licensing Daniel Himmelstein April 3, 2016 196 Completed
11
 Adding pathway resources to your network Daniel Himmelstein April 2, 2016 154 Completed
2
 The ADEPTUS resource for expression signatures of disease Daniel Himmelstein March 31, 2016 132 Completed
2
 Announcing PharmacotherapyDB: the Open Catalog of Drug Therapies for Disease Daniel Himmelstein March 15, 2016 307 Completed
16
 Expert curation of our indication catalog for disease-modifying treatments Pouya Khankhanian March 14, 2016 262 Completed
1
 Assessing the imputation quality of gene expression in LINCS L1000 Daniel Himmelstein March 11, 2016 199 Completed
5
 Positive correlations between knockdown and overexpression profiles from LINCS L1000 Daniel Himmelstein March 9, 2016 269 Open
14
 Workshop to analyze LINCS data for the Systems Pharmacology course at UCSF Daniel Himmelstein March 9, 2016 184 Completed
8
 Processing Bgee for tissue-specific gene presence and over/under-expression Daniel Himmelstein March 8, 2016 140 Completed
7
 Computing consensus transcriptional profiles for LINCS L1000 perturbations Daniel Himmelstein March 7, 2016 680 Completed
8
 UniChem Mapping to LINCS Small Molecules Daniel Himmelstein March 7, 2016 451 Completed
6
 Renaming ‘heterogeneous networks’ to a more concise and catchy term Daniel Himmelstein Jan. 28, 2016 200 Completed
2
 Licensing neo4j Daniel Himmelstein Jan. 11, 2016 320 In Progress
2
 Permuting hetnets and implementing randomized edge swaps in cypher Daniel Himmelstein Jan. 6, 2016 113 Deferred
4
 Path exclusion conditions Daniel Himmelstein Dec. 21, 2015 332 In Progress
6
 Python for the modern biodata scientist Daniel Himmelstein Dec. 2, 2015 988 Open
3
 Incomplete Interactome licensing Daniel Himmelstein Nov. 23, 2015 119 Completed
6
 Integrating drug target information from BindingDB Daniel Himmelstein Nov. 19, 2015 298 Completed
11
 Tissue-specific gene expression resources Daniel Himmelstein Nov. 4, 2015 826 Completed
2
 LINCS L1000 licensing Daniel Himmelstein Oct. 19, 2015 389 Completed
15
 Processing GTEx for tissue-specific gene expression Frederic Bastian Sept. 7, 2015 686 Declined
2
 R best practices Daniel Himmelstein Aug. 29, 2015 1110 Open
3
 Processing the DISEASES resource for disease–gene relationships Daniel Himmelstein Aug. 21, 2015 84 Completed
8
 Processing DisGeNET for disease-gene relationships Daniel Himmelstein Aug. 20, 2015 154 Completed
4
 Text as a resource for network population? Daniel Himmelstein Aug. 20, 2015 102 Accepted
3
 Extracting side effects from SIDER 4 Daniel Himmelstein Aug. 11, 2015 189 Completed
7
 Assessing the quality and applicability of the SIDER 2 resource Daniel Himmelstein Aug. 10, 2015 178 Completed
8
 The TISSUES resource for the tissue-specificity of genes Daniel Himmelstein Aug. 9, 2015 126 Completed
4
 Protein (target, carrier, transporter, and enzyme) interactions in DrugBank Daniel Himmelstein Aug. 5, 2015 994 Completed
3
 Calculating molecular similarities between DrugBank compounds Daniel Himmelstein Aug. 4, 2015 241 Completed
16
 Tissue Node Daniel Himmelstein Aug. 3, 2015 181 Completed
8
 Compiling Gene Ontology annotations into an easy-to-use format Daniel Himmelstein July 29, 2015 352 Completed
1
 Functional disease annotations for genes using DOAF Daniel Himmelstein July 14, 2015 87 Completed
1
 Disease similarity from MEDLINE topic cooccurrence Daniel Himmelstein July 14, 2015 90 Completed
2
 Extracting disease-gene associations from the GWAS Catalog Daniel Himmelstein July 9, 2015 306 Completed
3
 Selecting informative ERC (evolutionary rate covariation) values between genes Daniel Himmelstein June 16, 2015 103 Completed
2
 KaBOB Knowledgebase Daniel Himmelstein May 9, 2015 133 Declined
5
 Unifying drug vocabularies Daniel Himmelstein May 5, 2015 430 Completed
3
 Extracting indications from the ehrlink resource Daniel Himmelstein May 5, 2015 111 Completed
4
 Retrieving the ingredients in RxNorm concepts Antoine Lizee May 1, 2015 682 Completed
4
 Human Symptom Disease Network-MeSH ID Matching Daniel Himmelstein April 30, 2015 383 Completed
2
 Mapping Incomplete Interactome disease names to MeSH Daniel Himmelstein April 29, 2015 73 Completed
5
 Processing LabeledIn to extract indications Daniel Himmelstein April 8, 2015 147 Completed
9
 Enabling reproducibility and reuse Daniel Himmelstein March 20, 2015 139 Open
2
 MEDI indications data — discrepancy in resource-specific counts Daniel Himmelstein Feb. 17, 2015 109 Completed
5
 Seeking an open source implementation of the Gerstein-Sonnhammer-Chothia Algorithm Antoine Lizee Jan. 26, 2015 184 Completed
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