India partnering award: Sustainable data archiving and dissemination strategy to support data driven biology
Lead Research Organisation:
European Bioinformatics Institute
Department Name: MSCB Macromolec, structural and chem bio
Abstract
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Publications
PDBe-KB Consortium
(2020)
PDBe-KB: a community-driven resource for structural and functional annotations.
in Nucleic acids research
WwPDB Consortium
(2024)
EMDB-the Electron Microscopy Data Bank.
in Nucleic acids research
| Description | A number of Structural Bioinformatics teams from India are now collaborating with PDBe and providing their data to PDBe-KB resources. Follow on workshops and exchange visits will continue in the years 2020 and 2021. The Indian partners have also proceeded with establishing PDB India, efforts supported by PDBe and its wwPDB partners. |
| Exploitation Route | The partnering award between PDBe and Indian Structural Bioinformatics teams will explore potential infrastructure solutions that will (1) benefit users of PDBe services through offering richer data, and (2) give greater exposure to collaborators who would be sharing their unique data through this infrastructure. |
| Sectors | Agriculture Food and Drink Healthcare Pharmaceuticals and Medical Biotechnology |
| Description | Indian funding agencies are actively funding the development of data management infrastructure. The PDB-India efforts are informing the policies adopted by the Indian funding agencies on managing structural data. The project has also informed the development of worldwide Protein Data Bank policies on engagement with new partners. |
| First Year Of Impact | 2023 |
| Sector | Digital/Communication/Information Technologies (including Software) |
| Impact Types | Policy & public services |
| Description | Bhattacharyya - nu_param |
| Organisation | Saha institute of nuclear physics |
| Country | India |
| Sector | Academic/University |
| PI Contribution | n/a |
| Collaborator Contribution | Our partners have contirbuted a software package to analyse and report structural parameters pertaining to nucleic acids (RNA/DNA). This was lacking in our current pipelines. |
| Impact | Too early to tell |
| Start Year | 2018 |
| Description | A presentation at National Institute of Immunology, Delhi |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | The presentation included information on the PDB archive management by the wwPDB and its associate members. It also described the work done at PDBe on enriching the macromolecular structure data with structural and functional annotations for complexes, domains and small molecule ligands. The impact of AlphaFold was discussed, and the infrastructure developments to support the use of predicted models were described. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&ved=2ahUKEwjj4Oero9-EAxXBTEEAHQGGDPgQ... |
| Description | Annual PDBe-KB meeting - 2018 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The first in a series of annual workshops, where the progress of the PDBe-KB resource was reported, including the developments of the FunPDBe project. Two participants from India (NII, New Delhi and IISER Pune, Pune) attended the workshop and plans were made on their participation in the PDBe-KB/FunPDBe activities. Since then, one of the Indian teams have contributed their data to the resource. In addition, prior and new partners from the UK (UCL, Univ Kent, ICR, Univ Dundee), Italy (Univ Rome) and Belgium (VIB/VUB) have contributed their data, while some attendees from the UK, Czech Rep and Spain committed to providing data at a later stage. |
| Year(s) Of Engagement Activity | 2018 |
| Description | FunPDBe WP2 progress |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Annual meeting to discuss the progress of the FunPDBe project. |
| Year(s) Of Engagement Activity | 2019 |
| Description | IBDC visit |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | A visit to Indian Biological Data Centre to discuss data management |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.linkedin.com/posts/sonia-balyan-2092a145_its-always-great-to-interact-with-visionary-act... |
| Description | Indian Biophysical Society-PDBe workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | This workshop was conducted as part of the Indian Biophysical Society meeting at the Indian Institute of Science Education and Research (IISER), India. |
| Year(s) Of Engagement Activity | 2018 |
| Description | PDBe/Uniprot API workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This workshop was conducted at the National Institute of Immunology in India and involved 50 international participants. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Talk at IISER (Pune) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A presentation on PDBe, pdbe.org website and the infrastructure behind it, including SIFTS. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Talk at MBU (Bengaluru) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | A presentation on PDBe, pdbe.org website and the infrastructure behind it, including SIFTS, API and search functionality. The talk was attended by over 50 people from the Molecular Biophysics Unit and other departments of the IISc in Bengaluru, India. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Talk at NII (New Delhi) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A presentation on PDBe, pdbe.org website and the infrastructure behind it, including SIFTS. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Talk at Pune University (Pune) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | A presentation on PDBe, pdbe.org website and the infrastructure behind it, including SIFTS. |
| Year(s) Of Engagement Activity | 2017 |