China Partnering Award: Proteomics Data Exchange
Lead Research Organisation:
European Bioinformatics Institute
Department Name: Proteomics Services Team
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Publications
Dass G
(2020)
The Omics Discovery REST interface
Dass G
(2020)
The omics discovery REST interface.
in Nucleic acids research
Deutsch EW
(2021)
Universal Spectrum Identifier for mass spectra.
in Nature methods
Deutsch EW
(2017)
Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.
in Journal of proteome research
Deutsch EW
(2020)
The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics.
in Nucleic acids research
Ma J
(2019)
iProX: an integrated proteome resource.
in Nucleic acids research
Perez-Riverol Y
(2019)
Quantifying the impact of public omics data
in Nature Communications
| Description | Support from this grant has allowed us to organise the annual meeting of the HUPO Proteomics Standards Initiative in Beijing in Beijing, and to train members of the iProx database team at the National Center for Protein Sciences, Beijing, in the setup and operation of iProx, an open access proteomics database. iProx has become a member of the international ProteomeXchange consortium and has been published recently in the NAR Database Issue (PMID:30252093). iProx is now regularly releasing proteomics data from Chinese research teams to the global scientific public. In the current climate of difficult international collaboration with China, I consider it a significant success in science policy to contribute to an open data approach in the Chinese Proteomics Community. In 2019/2020, we have started to extend concepts from ProteomeXchange to the domain of systems biology models. EMBL-EBI is hosting an international "Harmony" hackathon-style workshop (03/2020), which is focussed on implementation of standards in systems biology, and on establishing ModeleXchange as a systems biology counterpart to ProteomeXchange. Part of the technical infrastructure will be provided by OmicsDI.org. Unfortunately, due to the COVID-19 outbreak, all in-person participation by our Chinese collaborators had to be cancelled. The workshop was the last in-person workshop that took place at EMBL-EBI before the lockdown. We have been granted a one year extension of the grant by UKRI. As of 3/2021, no additional funds have been spent in this period, as they are exclusively travel funds. However, development of ModeleXchange concepts has progressed, we currently have a pending UKRI BBR grant proposal. While the project is not specific to Chinese participation, we hope to be able to actively involve Chinese collaborators, remotely or in-person. |
| Exploitation Route | Membership of iProx in ProteomeXchange supports more efficient international dissemination of proteomics datasets generated in China, as well as better access of Chinese researchers to datasets published in other ProteomeXchange member databases. The membership of iProx in the international ProteomeXchange consortium also has a model character for Chinese resources joining international collaborations in other biomedical domains. Active discussions are currently going on for INSDC (Nucleotide sequences) and PDB (3D molecular structures). |
| Sectors | Agriculture, Food and Drink,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology |
| URL | https://www.ncbi.nlm.nih.gov/pubmed/28849660 |
| Description | Support from this grant has allowed us to organise the annual meeting of the HUPO Proteomics Standards Initiative in Beijing in Beijing, and to train members of the iProx database team at the National Center for Protein Sciences, Beijing, in the setup and operation of iProx, an open access proteomics database. iProx has become a member of the international ProteomeXchange consortium and has been published in the NAR Database Issue (PMID:30252093). From publication in 2018 to now (3/2023), the publication has received 681 citations (Google Scholar). The iProX paper was selected as one of China's 100 most influential international academic papers in 2019 (https://news.sina.com.cn/c/2020-12-30/doc-iiznezxs9689672.shtml). iProx is now regularly releasing proteomics data from Chinese research teams to the global scientific public. In the current climate of difficult international collaboration with China, I consider it a significant success in science policy to contribute to an open data approach in the Chinese Proteomics Community. |
| First Year Of Impact | 2018 |
| Sector | Agriculture, Food and Drink,Healthcare,Pharmaceuticals and Medical Biotechnology |
| Impact Types | Policy & public services |
| Title | iProx |
| Description | iProX is an integrated proteome resources center in China, which is built to accelerate the worldwide data sharing in proteomics. iProX is composed of a data submission system and a proteome database. The submission system is established under the guidance of the data-sharing policy made by ProteomeXchange consortium. Registered users can submit their proteomic datasets to iProX in public or private modes. Once an associated manuscript has been published, a dataset becomes automatically public. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | While iProx has been in existence for several years, the intensive consulting and development with support of the China Collaboration Grant has allowed it to reach the required standard to participate in the international ProteomeXchange consortium. Data deposition in a ProteomeXchange member database is required by many proteomics journals as part of the publication process. With a local ProteomeXchange member database, public dissemination of proteomics datasets has become much easier for Chinese scientists, and their contributions have become much more accessible to the international scientific community. |
| URL | http://www.iprox.org/ |
| Description | iProx |
| Organisation | National Center for Protein Sciences |
| Country | China |
| Sector | Charity/Non Profit |
| PI Contribution | Intensive consulting in the development of iProx, a public repository for proteomics data. |
| Collaborator Contribution | Development, curation and maintenance of iProx, a public repository for proteomics data. |
| Impact | The iProx database became an official member of the international ProteomeXchange consortium in December 2017. EMBL-EBI co-founded ProteomeXchange in 2011, and, in collaboration with international partners, developed it into a successful public database collaboration, similar to the EMBL/GenBank/DDBJ (INSDC.ORG) partnership. As of today, ProteomeXchange (proteomexchange.org) has five members (PRIDE, EMBL-EBI; Passel/PeptideAtlas, ISB; MassIVE, UCSD; jPOST, Japan; iProx, Beijing). With the accession of iProx to ProteomeXchange the primary aim of the iProx China Collaboration Grant has been achieved. |
| Start Year | 2016 |
| Description | PSI Spring Meeting 2017 |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | The Proteomics Standards Initiative (PSI) of the Human Proteome Organization (HUPO) has now been developing and promoting open community standards and software tools in the field of proteomics for 15 years. Under the guidance of the chair, cochairs, and other leadership positions, the PSI working groups are tasked with the development and maintenance of community standards via special workshops and ongoing work. Among the existing ratified standards, the PSI working groups continue to update PSI-MI XML, MITAB, mzML, mzIdentML, mzQuantML, mzTab, and the MIAPE (Minimum Information About a Proteomics Experiment) guidelines with the advance of new technologies and techniques. Furthermore, new standards are currently either in the final stages of completion (proBed and proBAM for proteogenomics results as well as PEFF) or in early stages of design (a spectral library standard format, a universal spectrum identifier, the qcML quality control format, and the Protein Expression Interface (PROXI) web services Application Programming Interface). The 2017 PSI Spring Workshop was held in Beijing, China at the National Center for Protein Sciences, Beijing (Phoenix Center). The workshop was chaired by Eric Deutsch and the local organizer, Henning Hermjakob. The opening session featured presentations by researchers who have implemented the standards and formats developed by the PSI to further their research work or tool development. Henry Lam (Hong Kong University of Science and Technology) described his work developing applications using spectral libraries in proteomics. In his talk, Lam argued that the process of spectral library building can be improved by first clustering by similarity and then selecting high-quality and confidently identified clusters to be included in the library. Although clustering spectra by similarity is more computationally intensive than simply grouping spectra by identifications, this process is a more robust mechanism for quality control and the detection of errors in spectral libraries. Finally, given the important role of spectral libraries and archives as an information hub and shared community resource, he challenged the PSI to develop a standardized data interchange format, which is currently sorely lacking. Such a standardized format will greatly simplify software development and enable better integration and interoperability of workflows involving spectral libraries and archives. Jun Qin, Director of the Phoenix Center, updated the attendees on the status of proteomic sciences in China. The Phoenix Center groups have achieved fast proteome sequencing, although there is still an issue with low abundance proteins, which first need to be enriched in a sample. The institute is developing Firmiana, a one-stop proteomic cloud platform for data analysis and processing.8 The aim is to reduce the cost of medicine, with the China Human Proteome Project (CNHPP) focusing on the 10 cancers most prevalent in China. The chairs from the different working groups gave an update on their activities, including nonpurely PSI activities such as ProteomeXchange and the status of metabolomics data standards. The workshop then split into parallel work-tracks for each of the developing formats and standards for the next 2 days, combining presentations with discussion and hands-on development work. A final plenary session reviewed the results of the working groups' activities at the end of the workshop. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.psidev.info/content/hupo-psi-meeting-2017 |