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 v Harvester PP presentation: Chris Mungall, Lawrence Berkeley National Laboratory: Distributed Data Discovery using GitHub, YAML and Markdown v Updates of last meeting action items v Brief updates from All Supported by the NIH grant 1U24 AI to the University of California, San Diego 2
3 Updates Action Items v Visit datamed.biocaddie.org and provide feedback for the new version, v0.2 via the prototype_issues repository in GitHub v Diagram showing biocaddie with Aztec and Repositories. CEDAR to be added to the diagram and shared with the group Jeff/Ian v Abstract submission deadline extended to 10/23, will send draft tomorrow to the group - Anu Supported by the NIH grant 1U24 AI to the University of California, San Diego 3
4 BioCADDIE Harvester Project: Distributed Data Discovery using GitHub, YAML and Markdown Chris Mungall Lawrence Berkeley Na6onal Laboratory
5 Well it could be worse, at least I m not doing metadata
6 How can we make it easier to a>ach Even fun? Idea: metadata? Target tech- savvy subset of data providers Provide guidelines and tooling that mesh with with their work habits If it works, extend to a wider variety of providers
7 Outline Background Observa6ons on metadata, code and datasets Preliminary related work: OBO Foundry Ontology Registry Global Bio6c Interac6ons (GloBI) Approach Vision Milestones (Now March 2016)
8 Coders love providing metadata Can we get dataset providers to share this love?
9
10 (1) Experience with the Open Biomedical Ontologies (OBO) Registry Background: High quality ontology metadata for ~100 ontologies Curated by OBO team (unfunded) Problem Metadata format lacked richness and extensibility Metadata could not be directly edited by ontology providers
11 (1) Experience with the Open Biomedical Ontologies (OBO) Registry Solu6on h>p://obofoundry.github.io/ Manage metadata files on GitHub Use YAML embedded in Markdown Anyone can submit a Pull Request Changes instantly visible using GitHub pages
12 Pull Requests allow for transparent distributed asynchronous edi6ng of content
13
14 (2) Experience with GloBI h>p://globalbio6cinterac6ons.org/ A search tool for finding species interac6on data What fungi infect bats in SW USA? Indexes 12m species- interac6ons from 15k studies Sources: inaturalist, Dryad, specialist databases, random websites, ad- hoc formats V1: Adding a new datasource required changing the centralized data inges6on code Problem: How to decentralize dataset contribu6ons
15 (2) Experience with GloBI Solu6on Simple metadata file specifica6on globi.json file Goes in top level of a github repository JSON(LD) Data can be in same repo, or external (e.g. dryad) Typically CSV GloBI central database periodically harvests data
16 Approach for biocaddie Harvester project Define format for a simple file that can be included in the root project directory YAML/Markdown Can be placed In the same directory tree as the data Externally, with a pointer to external data (e.g. figshare, dryad) Leverage GitHub social coding ecosystem for Distributed edi6ng of metadata files Cloud- based valida6on (Travis- CI) Pilot project Select exis6ng datasets and apply Demonstrate ability to search
17 researcher producing data (large dataset) deposits checks creates Travis-CI validation/ conversion SPARQL queries semweb user DataSet C DataSet B Cloud Storage / NIH Commons / Git LFS etc describes YAML Repo B YAML DataSet A GitHub / GitLab etc Repo A conversion JSON-LD / RDF HCLS compliant Linked Data Cloud content --- title: skin microbe analysis author: orcid: name: Carrie github: carriemicrobe types: - microbiome - computational datasets: - id: site: axilla - id: site: oral --- my notes here... Example YAML embedded in Markdown BioCaddie Harvester generates Data Index Search Service BioCADDIE creates + deposits finds via biocaddie searches researcher producing data (small dataset)
18 Current Progress and Project Current loca6on: Repository h>ps://github.com/cmungall/biocaddie- gym [Ques6on for biocaddie CDT: Should this move to a biocaddie github org?] Milestones: h>ps://github.com/cmungall/biocaddie- gym/ milestones Await project ini6a6on
19 Milestone 1: YAML Schema Goal: Define the format of a biocaddie.yml file that people can add to the top level of a directory Either the same directory that contains project data Or a pointer to it Why YAML? Simple, easy to author Extensible and nestable Can be embedded inside markdown files Superset of JSON (so can use JSON- LD) YAML- LD Automa6c equivalence to JSON- LD and to RDF Coordinate this with HCLS h>p:// dataset h>ps://github.com/cmungall/biocaddie- gym/milestones/yaml%20schema --- title: skin microbe analysis author: orcid: name: Carrie github: carriemicrobe types: - microbiome - computational datasets: - loc: ds1.tsv site: axilla - loc: ds2.tsv site: oral --- my notes here...
20 researcher producing data (large dataset) creates + deposits deposits creates researcher producing data (small dataset) DataSet C DataSet B Cloud Storage / NIH Commons / Git LFS etc describes YAML Repo B YAML DataSet A GitHub / GitLab etc Repo A content --- title: skin microbe analysis author: orcid: name: Carrie github: carriemicrobe types: - microbiome - computational datasets: - loc: ds1.tsv site: axilla - loc: ds2.tsv site: oral --- my notes here...
21 Milestone 2: biocaddie yaml validator Goal: Ensure biocaddie.yml files are syntac6cally and structurally valid Consistent with W3C HCLS Dataset descrip6on profile Prevent accidental typos that could hamper indexing efforts Approach: Write a simple python validator Integrate this with the GitHub travis con6nuous integra6on system h>ps://github.com/cmungall/biocaddie- gym/milestones/validator
22 researcher producing data (large dataset) deposits checks creates Travis-CI validation/ conversion DataSet C DataSet B Cloud Storage / NIH Commons / Git LFS etc describes YAML Repo B YAML DataSet A GitHub / GitLab etc Repo A
23
24 Goal: Milestone 3: Ultra- lite publishing framework Allow metadata providers to see the authored metadata in a less geeky format Approach: Create HTML templates for rendering dataset descrip6on YMLs using GitHub Pages / Jekyll framework h>ps://github.com/cmungall/biocaddie- gym/milestones/publishing
25 Milestone 4: Searchable index Goal: Demonstrate findability and searchability Approach: Query over git hos6ng sites for any repos that have biocaddie.{yml,md} file Index [Q: How involved should the biocaddie CDT be involved here?] h>ps://github.com/cmungall/biocaddie- gym/milestones/searchable%20index
26 Milestone 5: Pilot project Pilot project using exis6ng published datasets already in GitHub Datasets TBD Open to sugges6ons from biocaddie groups? Possibili6es: Exis6ng datasets indexed by h>p://monarchini6a6ve.org Exis6ng datasets on GitHub Evaluate h>ps://github.com/cmungall/biocaddie- gym/milestones/pilot
27 What next? Will this scale? Goals of pilot: Demonstrate feasibility with tech- savvy users Next steps, making it more accessible: [to be aligned with overall biocaddie goals] Provide authoring tools Integrate with dataset repositories (figshare, dryad) Work with git{hub,lab} to make more accessible?
28 Ongoing work Task Status 1 Metadata Ingestion Import repositories PDB,GEO 2. LINCS 3. BioProject, ArrayExpress, GEMMA, dbgap 4. ICPSR Stable API details Ongoing Sample files 1.2 Metadata mapping Ongoing 1.3 Metadata management Ongoing 1.4 Indexing Ongoing 2 Terminology server 2.1 Develop terminology server 1) Imported terminologies (6) and validated them 2) Created UI-Browser for TS 3) Integration to Scigraph API 4) Create auto complete feature 09/01 10/09 Ongoing 10/ Integrate terminology server Ongoing Supported by the NIH grant 1U24 AI to the University of California, San Diego 28
29 Pilot project integration (Task 3) PP Presented to CDT / / / /01 As Integrated Specialized advanced search for GWAS datasets Ranking function based on citation metrics for GEO series data a) isee similarity metric in ElasticSearch b) DELVE implementation as exploratory search and visualization option. (i) for PDB (ii) for gene expression data Ranking function based on citation metrics (dataset mentions) for PDB data Completed On 09/22 Ongoing (10/22) 9/01 Ongoing (11/10) Ongoing (10/27) Supported by the NIH grant 1U24 AI to the University of California, San Diego 29
30 Ongoing work Task Status 4 Interface Design 4.1 Global statistics Implemented 4.2 Design interface Ongoing 4.3 Implement new design Ongoing 4.4 Breadcrumb for website navigation Not started 4.5 Display most Accessed Datasets Not Started 5 Personalized search 5.1 Search history Implemented 5.2 Save search results Not Started 5.3 Share search results Not Started 5.4 User account - - Discussion Not Started 6 Searching/Ranking algorithms 6.1 Similar datasets Implemented 6.2 Data repositories search Ongoing 6.3 Boolean/advanced search Not Started 6.4 Refine search results based on user s selection Not Started Supported by the NIH grant 1U24 AI to the University of California, San Diego 30
31 Ongoing work Task Status 7 Display of results 7.1 Sort datasets Ongoing 7.2 Browsing (grouping facets/metadata) Not started 7.3 Accessibility information Not started 8 Link to external resources 8.1 Pubmed Ongoing 8.2 Grants Not Started 9 Feedback 9.1 GitHub Implemented 9.2 Feedback form Not Started 10 Documentation 10.1 Source code Not Started 10.2 Tutorials Not Started 11 Usability studies 11.1 UI Analysis Completed 11.2 User studies Not Started 12 Data Duplication issue Supported by the NIH grant 1U24 AI to the University of California, San Diego 31
32 Other issues v Please deposit codes in GitHub. Please contact me at Anupama.E.Gururaj@uth.tmc.edu if you need access v Any other issues? v 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
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
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
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
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
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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
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
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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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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
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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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