Core Technology Development Team Meeting
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1 Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: Access Code: For international call in numbers, please visit:
2 Agenda Updates on action items DataMed Evaluation LinkOut update Inclusion of more repositories into DataMed : plan and course of action DataMed v1.5 release before BD2K AHM Updates from all team members Supported by the NIH grant 1U24 AI to the University of California, San Diego 2
3 Updates- action items Generate a HELP and FAQ page please start adding material here ASAP Robust server to host biocaddie to be set up ongoing work by Jeff and Claudiu Feedback on video Pilot Project Integration Supported by the NIH grant 1U24 AI to the University of California, San Diego 3
4 Evaluation on Benchmark Datasets Xiaoling Chen
5 Benchmark Datasets Datasets: (before V0.5) Repositories: 20 Test queries: 15 Index of benchmark dataset
6 Example of query Query 4: Find all data types related to inflammation during oxidative stress in human hepatic cells across all databases Keywords Query: inflammation oxidative stress human hepatic cells Expanded Query: inflammation oxidative stress human hepatic cells Chronic inflammatory reaction morphologic abnormality cell infiltration arthritis disorder Oxidative Stresses Human Homo sapiens organism Man Tympanic cells set Cellulae tympanicae Mother Cell Stem cell Unit Colony Forming Progenitor
7 Queries Natural query 1 Find protein sequencing data related to bacterial chemotaxis across all databases 2 Search for data of all types related to MIP-2 gene related to biliary atresia across all databases 3 Search for all data types related to gene TP53INP1 in relation to p53 activation across all databases 4 Find all data types related to inflammation during oxidative stress in human hepatic cells across all databases 5 Search for gene expression and genetic deletion data that mention CD69 in memory augmentation studies across all databases 6 Search for data of all types related to the LDLR gene related to cardiovascular disease across all databases 7 Search for gene expression datasets on photo transduction and regulation of calcium in blind D. melanogaster 8 Search for proteomic data related to regulation of calcium in blind D. melanogaster keyword Protein sequencing bacterial chemotaxis Mip-2 biliary atresia TP53INP1 p53 activation inflammation oxidative stress human hepatic cells CD69 memory augmentation LDLR gene cardiovascular disease photo transduction regulation calcium blind D melanogaster proteomic data regulation calcium blind Drosophila melanogaster
8 Queries Natural query 9 Search for data of all types related to the ob gene in obese M. musculus across all databases 10 Search for data of all types related to energy metabolism in obese M. musculus 11 Search for all data for the HTT gene related to Huntingtonís disease across all databases 12 Search for data on neural brain tissue in transgenic mice related to Huntingtonís disease 13 Search for all data on the SNCA gene related to Parkinsonís disease across all databases 14 Search for data on nerve cells in the substantia nigra in mice across all keyword ob gene obese Mus musculus energy metabolism obese Mus musculus HTT gene Huntington disease neural brain tissue Huntington disease transgenic mice SNCA gene Parkinson Disease nerve cells substantia nigra mice
9 Which records are annotated? For each query, query in two versions, keywords version and expansion query in four search engines (Lucence, Indri, Terrier, SemanticVectors) Get first 300 results from each search engine, combine and delete the duplicated ones. For each query, maximum 2400 (300*4*2) records are annotated.
10 Gold Standard (Annotated results) id annotated relevant partial relevant not relevant
11 Trec_eval tool A standard tool used by the TREC community for evaluating an ad hoc retrieval run, given the results file and a standard of judged results. Metrics: Name infap infndcg ip@n Prec@rec 11 points Explanation inferred Average Precision. A commonly used measure by information retrieval community (based on random sampling) Inferred normalized discounted cumulated gain. A commonly used measure that incorporates graded relevance judgments. Precision after N retrieved Interpolated recall-precision averages at n recall n = [0.00, ,0.30,0.40,0.50,0.60,0.70,0.80,0.90,1.
12 Search in _all field using default TF-IDF algorithm in ES, retrieve first 300 records query infap infndcg all TREC 2014 CDS track 30 topics Top Top infap infndcg P@
13 Different Search engines Search Engine (basic query) infap infndcg ElasticSearch Lucene Terrier Indri Semantic Search Engine (expanded query) infap infndcg ElasticSearch Lucene Terrier Indri Semantic
14 Fields 187 unique fields in the benchmark dataset Run search on each field, w 11 fields is in integer or date format, cannot be searched using terms (METADATA.FemaleNum, METADATA.dataItem.releaseDate, METADATA.dataItem.depositionDate, etc) w 68 fields does not return results (METADATA.organization.homePage, METADATA.dataset.dateAccession, METADATA.internal.rank, METADATA.datastandard.license, etc) w 108 fields return results
15 Search on important fields Search field infap infndcg TITLE description Mulit_fields (Title and description) Multi_match, cross_fields Mulit_fields (Title and description) Multi_match,cross_fields,title^ _all _all (concatenate only title and description) _all (concatenate Special _all the field 108 fields that returned Combines results) the original values from each field as a string. The distinction between field lengths disappears in the _all field. The shorter the field, the more important.
16 Next steps Try different similarity algorithms in ES (BM25, LMD, DFR, etc) Explore different parameters in the query. Try boost in the query components and query fields. Expand synonyms using NLP server Try different relationship between synonyms
17 LinkOut Update - Databases available for linking
18 LinkOut update Meeting with Kathy Kwan Pubmed to be the first try Kathy sent us provider ID & ftp site We will provide sample data Supported by the NIH grant 1U24 AI to the University of California, San Diego 18
19 Inclusion of more repositories into DataMed : plan and course of action DK3ParoPWewow5lmqlGJKQc0/edit#gid=0 0BsVdI_tddAXZrXS5eQc8K8/edit#gid= Each site should get at least 2 repos mapped/team per week Progress to be reported every CDT meeting with plans for next set of repos for mapping Supported by the NIH grant 1U24 AI to the University of California, San Diego 19
20 DATS 2.1 Mapping UCSD - DBMI UTHealth UCSD CRBS Recently Completed LSDB, NDAR, HMP, American Gut Project (in EBI), IRD-JCVI, GeneNetwork Retina, EMDB, BMRB, TCGA, NBIA, Epigenomics, RGD, ClinVar, Vectorbase, IntAct (10) YPED, Uniprot - Swisprot, CIL, NURSA, ICPSR, Neuromorpho, openfmri, NIDDK CR, Physiobank, CIA-Datacite, ICPSR, PeptideAtlas, CVRG, Gemma, GEO, ArrayExpress, CTN, LINCS,PDB, NeuroVault Results, NeuroVault Atlas, NeuroVault Collections, MPD, ProteomeXChange, NITRC, ASCB Cell Image Library (25) Currently Working On Nature Scientific SRA, Dryad, Clinical Trials, dbgap, Phenogen Informatics, Human Proteinpedia (6) Uniprot Trembl, bioproject, Datacite Biomedical Repositories (30 selected based on content) (33) Up Next Waiting for new assignment EuPathDB, Diabetic Retinopathy Clinical Research Network, Diabetes Research in Children Network, Candida Genome Database (4) EU Clinical Trials Network, OmicsDI, (4) Waiting on repository response SimTK, EuPathDB Mendeley Data (OAuth connection), IMEx (waiting for source data feed), ImmPort (Contacted source for feed info), Cancer Nanotechnology Laboratory portal (Contacted source) Supported by the NIH grant 1U24 AI to the University of California, San Diego
21 DataMed Ingestion UCSD - DBMI UTHealth UCSD CRBS Recently Completed LSDB, GeneNetwork Retina, EMDB, Epigenomics, ClinVar, BMRB, TCGA (4) YPED, Uniprot - Swisprot, CIL, NURSA, ICPSR, Neuromorpho, openfmri, NIDDK CR, Physiobank, CIA-Datacite, ICPSR, PeptideAtlas, CVRG, Gemma, GEO, ArrayExpress, CTN, LINCS,PDB, NeuroVault Results, NeuroVault Atlas, NeuroVault Collections, MPD, ProteomeXChange, NITRC, ASCB Cell Image Library (25) Currently Working On AmericanGut, (EBI), HMP, NDAR NSRR, RGD, Vectorbase, IntAct (4) Uniprot Trembl, bioproject, Datacite Biomedical Repositories (30 selected based on content) (33) Up Next IRD (JCVI), NatureScientific Phenogen Informatics, Human Proteinpedia, Diabetic Retinopathy Clinical Research Network, Diabetes Research in Children Network, Candida Genome Database (5) EU Clinical Trials Network, OmicsDI (2) Waiting on repository response SimTK, EuPathDB Mendeley Data (OAuth connection), IMEx (waiting for source data feed), ImmPort (Contacted source for feed info), Cancer Nanotechnology Laboratory portal (Contacted source) Supported by the NIH grant 1U24 AI to the University of California, San Diego
22 DataMed release DataMed v1.5 release before BD2K AHM: w Increased number of repositories mapped to DATS 2.1 : target ~ 40 repos mapped to DATS 2.1 w Additional functions sorting Visualization user activity tracking NLP at backend UI functionality needs testing before release November 17 th Release on November 22 nd Supported by the NIH grant 1U24 AI to the University of California, San Diego 22
23 Github Issues Total Issues 158 Number Open 58 Number Closed 100 Associated with v1.0 Number Open 12 Number Closed 8 Usability Issues Number Open 23 Number Closed 10 Associated with v0.5 Number Open 23 Number Closed 63 Number of Bugs Number Open 5 Number Closed 12 Number of Enhancements Number Open 21 Number Closed 28 Number of Questions Number Open 9 Number Closed 11 Number of Help Wanted Number Open 3 Number Closed 0 Supported by the NIH grant 1U24 AI to the University of California, San Diego 23
24 Ongoing work Task Supported by the NIH grant 1U24 AI to the University of California, San Diego Status 1 Metadata Ingestion 1.1 Import repositories expansion Ongoing 1.2 Data repository suggestion form at DataMed George/Xiaoling / Sanda Ongoing 1.3 Metadata mapping review/ reconciliation between curators Ongoing 1.4 Metadata management Ongoing 1.5 Indexing Ongoing 1.6 NLP-based indexing : Gene/protein, Disease, Drug/chemical, Biological process, Organism, Format, Implemented at backend Access, Cell types 1.7 Bulk download of indices Not Started 2 Terminology server 2.3 Integrate terminology server (Indexing) Ongoing 4 Interface Design 4.2 Design interface usability issues Ongoing 4.5 Display most Accessed Datasets Not Started 24
25 Ongoing work Task Status 5 Personalized search 5.1 Improve the tracking system Ongoing 6 Searching/Ranking algorithms 6.1 Similar datasets to be expanded Ongoing 7 Display of results 7.1 Sort datasets author, published date, repository, title Ongoing 7.2 What fields should be displayed? Ongoing Additional filters: File type Data Restrictions (data use agreement, restricted, unrestricted) Data Level (participant/aggregate) 7.3 Population (mouse, human, etc) 8 Link to external resources 1. Pubmed: click through to pubmed records of citing publications: copy citation to clipboard Scholix Framework for Linking Data and Literature 3. Linkout Not started Not Started Supported by the NIH grant 1U24 AI to the University of California, San Diego 25
26 Ongoing work Task Status 10 Documentation 10.1 Source code Ongoing 10.2 Tutorials Not Started 10.3 Help menu Ongoing 10.4 Video Ongoing 11 Usability studies 11.2 User studies Ongoing Data Duplication issue: Create a plan for how to best display/represent the duplicate in the metadata records and set up a meeting to discuss the workflow for displaying the duplicates in the metadata records Jeff/Anu Additional field in index Generation of benchmark for the dataset Completed 14 Relationship Network Graph 15 Collaborative research support Supported by the NIH grant 1U24 AI to the University of California, San Diego 26
27 Other issues Please deposit codes in GitHub. Please contact me at if you need access hp Any other issues? Thank You
Core Technology Development Team Meeting
Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Executive Committee Meeting
Executive Committee Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Core Technology Development Team Meeting
Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Core Technology Development Team Meeting
Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Core Technology Development Team Meeting
Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Core Technology Development Team Meeting
Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Core Technology Development Team Meeting
Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Core Technology Development Team Meeting
Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Core Technology Development Team Meeting
Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Core Technology Development Team Meeting
Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Core Technology Development Team Meeting
Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Core Technology Development Team Meeting
Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Core Technology Development Team Meeting
Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Core Technology Development Team Meeting
Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Executive Committee Meeting
Executive Committee Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Core Technology Development Team Meeting
Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Core Technology Development Team Meeting
Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Metadata Ingestion and Processinng
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Executive Committee Meeting
Executive Committee Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Core Technology Development Team Meeting
Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Core Technology Development Team Meeting
Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Executive Committee Meeting
Executive Committee Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Steering Committee Meeting
Steering Committee Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Core Technology Development Team Meeting
Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Steering Committee Meeting
Steering Committee Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Steering Committee Meeting
Steering Committee Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please isit: https://www.readytalk.com/account-administration/international-numbers
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Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
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