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1.
Orchard S Albar JP Deutsch EW Binz PA Jones AR Creasy D Hermjakob H 《Proteomics》2008,8(20):4168-4172
The role of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) is to produce and release community-accepted reporting requirements, interchange formats and controlled vocabularies for mass spectrometry proteomics and related technologies such as gel electrophoresis, column chromatography and molecular interactions. A number of significant advances were made at this workshop, with the new MS standard, mzML, being finalised prior to release on 1(st) June 2008 and analysisXML, which will allow protein and peptide identifications and post-translational modifications to be captured, being prepared to enter the review process this summer. The accompanying controlled vocabularies are continuing to evolve and a number of standards papers are now being finalised prior to publication. 相似文献
2.
The plenary session of the Proteomics Standards Initiative of the Human Proteome Organisation provided an opportunity to update delegates on the progress of the work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO-PSI) to develop and implement standards in the field of proteomics. Significant advances have been made since the previous congress, with several of the interchange standards and minimal requirements documents being submitted for publication in the literature and being more widely adopted by both manufacturers and data repositories. An exciting development over the interim twelve months is the ongoing merger of the two existing mass spectrometry standards, the PSI mzData and Institute for Systems Biology mzXML, into a single product. This should be achieved by early in 2007. 相似文献
3.
This meeting was convened with the aim of bringing together representatives from scientific journals, granting authorities, software and instrumentation manufacturers, data producers and database providers to discuss the implementation and adoption of the HUPO-PSI data standards and how these can be best used to support the publication and dissemination of proteomics data. The current status of data formats and reporting requirements was reviewed and the attendees agreed that the use of data standards was essential as the field of proteomics grows and matures. 相似文献
4.
Orchard S Hermjakob H Taylor CF Potthast F Jones P Zhu W Julian RK Apweiler R 《Proteomics》2005,5(14):3552-3555
The spring workshop of the HUPO-PSI convened in Siena to further progress the data standards which are already making an impact on data exchange and deposition in the field of proteomics. Separate work groups pushed forward existing XML standards for the exchange of Molecular Interaction data (PSI-MI, MIF) and Mass Spectrometry data (PSI-MS, mzData) whilst significant progress was made on PSI-MS' mzIdent, which will allow the capture of data from analytical tools such as peak list search engines. A new focus for PSI (GPS, gel electrophoresis) was explored; as was the need for a common representation of protein modifications by all workers in the field of proteomics and beyond. All these efforts are contextualised by the work of the General Proteomics Standards workgroup; which in addition to the MIAPE reporting guidelines, is continually evolving an object model (PSI-OM) from which will be derived the general standard XML format for exchanging data between researchers, and for submission to repositories or journals. 相似文献
5.
Sandra Orchard Eric W. Deutsch Pierre‐Alain Binz Andrew R. Jones David Creasy Luisa Montechi‐Palazzi Garry Corthals Henning Hermjakob 《Proteomics》2009,9(19):4429-4432
The Human Proteome Organization Proteomics Standards Initiative has produced reporting requirements and data interchange formats for the proteomics community. The implementation of these increasingly mature formats was the main focus of this meeting, with extensions being made to many schema to enable encoding of new data types. The endorsement of the proteomics standards initiative standards by an increasing number of journals is a main driving force behind tool development and a recognized need to ease the process of data deposition into the public domain for the bench scientist. 相似文献
6.
Tang Taishan Xu Ye Wang Jianfeng Tan Xiao Zhao Xiaona Zhou Ping Kong Fande Zhu Changqing Lu Chengping Lin Huixing 《Functional & integrative genomics》2021,21(3):421-433
Functional & Integrative Genomics - This study analyzed the difference between biofilm and planktonic Brucella abortus using metabolomics and proteomics. Brucella abortus was cultured in... 相似文献
7.
The HUPO proteomics standards initiative--easing communication and minimizing data loss in a changing world 总被引:1,自引:0,他引:1
The amount of data currently being generated by proteomics laboratories around the world is increasing exponentially, making it ever more critical that scientists are able to exchange, compare and retrieve datasets when re-evaluation of their original conclusions becomes important. Only a fraction of this data is published in the literature and important information is being lost every day as data formats become obsolete. The Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) was tasked with the creation of data standards and interchange formats to allow both the exchange and storage of such data irrespective of the hardware and software from which it was generated. This article will provide an update on the work of this group, the creation and implementation of these standards and the standards-compliant data repositories being established as result of their efforts. 相似文献
8.
9.
S Orchard PA Binz C Borchers MK Gilson AR Jones G Nicola JA Vizcaino EW Deutsch H Hermjakob 《Proteomics》2012,12(18):2767-2772
The Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) was established in 2002 with the aim of defining community standards for data representation in proteomics and facilitating data comparison, exchange and verification. Over the last 10 years significant advances have been made, with common data standards now published and implemented in the field of both mass spectrometry and molecular interactions. The 2012 meeting further advanced this work, with the mass spectrometry groups finalising approaches to capturing the output from recent developments in the field, such as quantitative proteomics and SRM. The molecular interaction group focused on improving the integration of data from multiple resources. Both groups united with a guest work track, organized by the HUPO Technology/Standards Committee, to formulate proposals for data submissions from the HUPO Human Proteome Project and to start an initiative to collect standard experimental protocols. 相似文献
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11.
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics 总被引:1,自引:0,他引:1
Jones AR Miller M Aebersold R Apweiler R Ball CA Brazma A Degreef J Hardy N Hermjakob H Hubbard SJ Hussey P Igra M Jenkins H Julian RK Laursen K Oliver SG Paton NW Sansone SA Sarkans U Stoeckert CJ Taylor CF Whetzel PL White JA Spellman P Pizarro A 《Nature biotechnology》2007,25(10):1127-1133
The Functional Genomics Experiment data model (FuGE) has been developed to facilitate convergence of data standards for high-throughput, comprehensive analyses in biology. FuGE models the components of an experimental activity that are common across different technologies, including protocols, samples and data. FuGE provides a foundation for describing entire laboratory workflows and for the development of new data formats. The Microarray Gene Expression Data society and the Proteomics Standards Initiative have committed to using FuGE as the basis for defining their respective standards, and other standards groups, including the Metabolomics Standards Initiative, are evaluating FuGE in their development efforts. Adoption of FuGE by multiple standards bodies will enable uniform reporting of common parts of functional genomics workflows, simplify data-integration efforts and ease the burden on researchers seeking to fulfill multiple minimum reporting requirements. Such advances are important for transparent data management and mining in functional genomics and systems biology. 相似文献
12.
Orchard S Taylor CF Jones P Montechi-Palazzo L Binz PA Jones AR Pizarro A Julian RK Hermjakob H 《Proteomics》2007,7(3):337-339
Since its conception in April 2002, the Human Proteome Organisation Proteomics Standards Initiative has contributed to the development of community standards for proteomics in a collaborative and very dynamic manner, resulting in the publication and increasing adoption of a number of interchange formats and controlled vocabularies. Repositories supporting these formats are being established or are already operational. In parallel with this, minimum reporting requirement have been developed and are now maturing to the point where they have been submitted for journal publication after prolonged exposure to community-input via the PSI website. 相似文献
13.
Wang Shiliang Li Wenlu Yang Long Yuan Jianqiao Wang Lin Li Na Zhao Hongyu 《Functional & integrative genomics》2022,22(5):891-903
Functional & Integrative Genomics - Oral squamous cell carcinoma (OSCC) is a common malignant tumor occurring in the oral cavity. Circular RNAs (circRNAs) play a crucial regulatory role in many... 相似文献
14.
Orchard S Montechi-Palazzi L Deutsch EW Binz PA Jones AR Paton N Pizarro A Creasy DM Wojcik J Hermjakob H 《Proteomics》2007,7(19):3436-3440
Over the last five years, the Human Proteome Organisation Proteomics Standards Initiative (HUPO PSI) has produced and released community-accepted XML interchange formats in the fields of mass spectrometry, molecular interactions and gel electrophoresis, have led the field in the discussion of the minimum information with which such data should be annotated and are now in the process of publishing much of this information. At this 4(th) Spring workshop, the emphasis was on consolidating this effort, refining and improving the existing models and in pushing these forward to align with more broadly encompassing efforts such as FuGE (Jones, A.R., Pizarro, A., Spellman, P., Miller, M., FuGE Working Group FuGE: Functional Genomics Experiment Object Model. OMICS 2006, 10, 179-184) and the Ontology for Biomedical Investigation (OBI). The effort to merge the existing mass spectrometry XML interchange formats, mzData and mzXML, into one single standard mzML yielded significant progress. Also the preliminary design of AnalysisXML was extended to include several new use cases and better support for quantification information. Finally the Molecular Interaction group discussed the development of a molecular interaction scoring system with accompanying gold standard data test sets. 相似文献
15.
Wang Kai Wu Pingxian Chen Dejuan Zhou Jie Yang Xidi Jiang Anan Xiao Weihang Qiu Xiaotian Zeng Yangshuang Xu Xu Tang Guoqing 《Functional & integrative genomics》2021,21(5-6):655-664
Functional & Integrative Genomics - Here we used two kinds of chips data from 5 pig breeds, Chinese Duroc (DD), Landrace (LL), Yorkshire (YY), Liangshan (LS), and Qingyu pigs (QY) in China to... 相似文献
16.
Sinchaikul S Sookkheo B Topanuruk S Juan HF Phutrakul S Chen ST 《Journal of chromatography. B, Analytical technologies in the biomedical and life sciences》2002,771(1-2):261-287
The ability of bioinformatics to characterize genomic and proteomic sequences from bacteria Bacillus sp. for prediction of genes and proteins has been evaluated. Genomics coupling with proteomics, which is relied on integration of the significant advances recently achieved in two-dimensional (2-D) electrophoretic separation of proteins and mass spectrometry (MS), are now important and high throughput techniques for qualifying and analyzing gene and protein expression, discovering new gene or protein products, and understanding of gene and protein functions including post-genomic study. In addition, the bioinformatics of Bacillus sp. is embraced into many databases that will facilitate to rapidly search the information of Bacillus sp. in both genomics and proteomics. It is also possible to highlight sites for post-translational modifications based on the specific protein sequence motifs that play important roles in the structure, activity and compartmentalization of proteins. Moreover, the secreted proteins from Bacillus sp. are interesting and widely used in many applications especially biomedical applications that are the highly advantages for their potential therapeutic values. 相似文献
17.
《Molecular & cellular proteomics : MCP》2014,13(8):1905-1913
Quality control is increasingly recognized as a crucial aspect of mass spectrometry based proteomics. Several recent papers discuss relevant parameters for quality control and present applications to extract these from the instrumental raw data. What has been missing, however, is a standard data exchange format for reporting these performance metrics. We therefore developed the qcML format, an XML-based standard that follows the design principles of the related mzML, mzIdentML, mzQuantML, and TraML standards from the HUPO-PSI (Proteomics Standards Initiative). In addition to the XML format, we also provide tools for the calculation of a wide range of quality metrics as well as a database format and interconversion tools, so that existing LIMS systems can easily add relational storage of the quality control data to their existing schema. We here describe the qcML specification, along with possible use cases and an illustrative example of the subsequent analysis possibilities. All information about qcML is available at http://code.google.com/p/qcml. 相似文献
18.
Bhogireddy Sailaja Mangrauthia Satendra K. Kumar Rakesh Pandey Arun K. Singh Sadhana Jain Ankit Budak Hikmet Varshney Rajeev K. Kudapa Himabindu 《Functional & integrative genomics》2021,21(3-4):313-330
Functional & Integrative Genomics - Beyond the most crucial roles of RNA molecules as a messenger, ribosomal, and transfer RNAs, the regulatory role of many non-coding RNAs (ncRNAs) in plant... 相似文献
19.
Li Chuting Su Ru Wang Xiuyuan Huang Guiping Liu Yanjun Yang Juhua Yin Zhao Gu Chunming Fei Jia 《Functional & integrative genomics》2022,22(5):1031-1041
Functional & Integrative Genomics - Recent studies have suggested the potency of berberine (BBR) for multiple cancer treatments, including multiple myeloma (MM). However, the direct target and... 相似文献
20.
McNally R 《Proteomics》2008,8(2):222-224
On 23 and 24 July, 2007, the Centre for Economic and Social Aspects of Genomics (CESAGen) held its first sociomics workshop at the Wellcome Trust Genome Campus, Hinxton, UK. The topic was transformation of knowledge production. Participants included social scientists together with those working on different elements of the proteomics knowledge production-line, including core facilities, data repositories, large-scale projects, MS, search engines, reference databases, standardisation and public funding. Recurrent motifs included gear-heads, black boxes, uncertainty and getting back to biology. 相似文献