Data Deposition as an Integral Part of the Publication Process (2009)
Proteomics data has been available in published literature for approximately 15 years and, until very recently, its appearance in a journal manuscripts has been the only route for making the results...
Sandra Orchard, Weimin Zhu, All K. Julian, Henning Hermjakob, Rolf Apweiler
The Protein Standards Initiative (PSI) group of the Human Proteome Organisation (HUPO) has been tasked with the establishment of common standards for data exchange in the field of proteomics [1]. The...
Chatr-aryamontri, Andrew, Kerrien, Samuel, Khadake, Jyoti, Orchard, Sandra, Ceol, Arnaud, Licata, Luana, ...
Abstract Background In the absence of consolidated pipelines to archive biological data electronically, information dispersed in the literature must be captured by manual annotation. Unfortunately,...
Taylor, Chris F., Field, Dawn, Sansone, Susanna-Assunta, Aerts, Jan, Apweiler, Rolf, Asburner, Michael, ...
The Minimum Information for Biological and Biomedical Investigations (MIBBI) project provides a resource for those exploring the range of extant minimum information checklists and fosters coordinated...
Standardising Proteomics Data – the work of the HUPO Proteomics Standards Initiative (2008)
Sandra Orchard, Henning Hermjakob
The HUPO Proteomics Standards initiative has dedicated the last 6 years to the design and implementation of common data reporting andexchange standards enabling the transfer of proteomics data from...
The Protein Feature Ontology: a tool for the unification of protein feature annotations (2008)
Reeves, Gabrielle A., Eilbeck, Karen, Magrane, Michele, O'Donovan, Claire, Montecchi-Palazzi, Luisa, Harris, Midori A., ...
Motivation: The advent of sequencing and structural genomics projects has provided a dramatic boost in the number of uncharacterized protein structures and sequences. Consequently, many computational...
Orchard, Sandra, Hermjakob, Henning
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...
Chiang, Tony, Li, Nianhua, Orchard, Sandra, Kerrien, Samuel, Hermjakob, Henning, Gentleman, Robert, ...
Motivation: The IntAct repository is one of the largest and most widely used databases for the curation and storage of molecular interaction data. These datasets need to be analyzed by computational...
Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions (2007)
Kerrien, Samuel, Orchard, Sandra, Montecchi-Palazzi, Luisa, Aranda, Bruno, Quinn, Antony F, Vinod, Nisha, ...
Abstract Background Molecular interaction Information is a key resource in modern biomedical research. Publicly available data have previously been provided in a broad array of diverse formats,...
The implications of alternative splicing in the ENCODE protein complement (2007)
Tress, Michael L., Martelli, Pier L., Frankish, Adam, Reeves, Gabrielle A., Wesselink, Jan J., Yeats, Corin, ...
Alternative premessenger RNA splicing enables genes to generate more than one gene product. Splicing events that occur within protein coding regions have the potential to alter the biological...
New developments in the InterPro database (2007)
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, ...
InterPro is an integrated resource for protein families, domains and functional sites, which integrates the following protein signature databases: PROSITE, PRINTS, ProDom, Pfam, SMART, TIGRFAMs,...
Orchard, Sandra, Apweiler, Rolf, Barkovich, Robert, Field, Dawn, Garavelli, John S., Horn, David, ...
The theme of the third annual Spring workshop of the HUPO-PSI was proteomics and beyond and its underlying goal was to reach beyond the boundaries of the proteomics community to interact with groups...
Sandra Orchard, Paul Kersey, Henning Hermjakob, Rolf Apweiler
The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics and to facilitate data comparison, exchange and verification. Initially the fields...
Sandra Orchard, Paul Kersey, Weimin Zhu, Luisa Montecchi-Palazzi, Henning Hermjakob, Rolf Apweiler
The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics and to facilitate data comparison, exchange and verification. Rapid progress has...
S. Orchard, L. Montecchi-palazzi, H. Hermjakob, R. Apweiler, Sandra Orchard, Luisa Montecchi-palazzi, ...
Controlled vocabularies provide a roadmap through complex biological data. Proteomic data is increasing in volume and is currently poorly served by public repositories due to the large number of...
InterPro, progress and status in 2005 (2005)
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam,...
IntAct: an open source molecular interaction database (2004)
Hermjakob,Henning, Montecchi-Palazzi,Luisa, Lewington,Chris, Mudali,Sugath, Kerrien,Samuel, Orchard,Sandra, ...
IntAct provides an open source database and toolkit for the storage, presentation and analysis of protein interactions. The web interface provides both textual and graphical representations of...
IntAct: an open source molecular interaction database (2004)
Hermjakob, Henning, Montecchi-Palazzi, Luisa, Lewington, Chris, Mudali, Sugath, Kerrien, Samuel, Orchard, Sandra, ...
IntAct provides an open source database and toolkit for the storage, presentation and analysis of protein interactions. The web interface provides both textual and graphical representations of...
IntAct: an open source molecular interaction database (2004)
Hermjakob, Henning, Montecchi-Palazzi, Luisa, Lewington, Chris, Mudali, Sugath, Kerrien, Samuel, Orchard, Sandra, ...
IntAct provides an open source database and toolkit for the storage, presentation and analysis of protein interactions. The web interface provides both textual and graphical representations of...
Sandra Orchard, Paul Kersey, Henning Hermjakob, Rolf Apweiler
The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics and to facilitate data comparison, exchange and verification. Initially the fields...
Sandra Orchard, Paul Kersey, Weimin Zhu, Luisa Montecchi-Palazzi, Henning Hermjakob, Rolf Apweiler
The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics and to facilitate data comparison, exchange and verification. Rapid progress has...
Mulder, Nicola J., Apweiler, Rolf, Attwood, Terri K., Bairoch, Amos, Bateman, Alex, ...
The exponential increase in the submission of nucleotide sequences to the nucleotide sequence database by genome sequencing centres has resulted in a need for rapid, automatic methods for...
IntAct: an open source molecular interaction database
Hermjakob, Henning, Montecchi-Palazzi, Luisa, Lewington, Chris, Mudali, Sugath, Kerrien, Samuel, Orchard, Sandra, ...
IntAct provides an open source database and toolkit for the storage, presentation and analysis of protein interactions. The web interface provides both textual and graphical representations of...
InterPro, progress and status in 2005
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam,...
IntAct: an open source molecular interaction database
Hermjakob, Henning, Montecchi-Palazzi, Luisa, Lewington, Chris, Mudali, Sugath, Kerrien, Samuel, Orchard, Sandra, ...
IntAct provides an open source database and toolkit for the storage, presentation and analysis of protein interactions. The web interface provides both textual and graphical representations of...
InterPro, progress and status in 2005
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam,...
New developments in the InterPro database
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, ...
InterPro is an integrated resource for protein families, domains and functional sites, which integrates the following protein signature databases: PROSITE, PRINTS, ProDom, Pfam, SMART, TIGRFAMs,...
The implications of alternative splicing in the ENCODE protein complement
Tress, Michael L., Martelli, Pier Luigi, Frankish, Adam, Reeves, Gabrielle A., Wesselink, Jan Jaap, Yeats, Corin, ...
Alternative premessenger RNA splicing enables genes to generate more than one gene product. Splicing events that occur within protein coding regions have the potential to alter the biological...
Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions
Kerrien, Samuel, Orchard, Sandra, Montecchi-Palazzi, Luisa, Aranda, Bruno, Quinn, Antony F, Vinod, Nisha, ...
Orchard, Sandra, Kersey, Paul, Hermjakob, Henning, Apweiler, Rolf
The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics and to facilitate data comparison, exchange and verification. Initially the fields...
Orchard, Sandra, Kersey, Paul, Zhu, Weimin, Montecchi-Palazzi, Luisa, Hermjakob, Henning, Apweiler, Rolf
The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics and to facilitate data comparison, exchange and verification. Rapid progress has...
Chatr-aryamontri, Andrew, Kerrien, Samuel, Khadake, Jyoti, Orchard, Sandra, Ceol, Arnaud, Licata, Luana, ...
Quintaje, Silvia Braconi, Orchard, Sandra
Biomolecule phosphorylation by protein kinases is a fundamental cell signaling process in all living cells. Following the comprehensive cataloguing of the protein kinase complement of the human...
The guest editor (AM) provides his perspective on the most recent advances on nucleoside diphosphate kinase (NDPK, otherwise known as AWD or NM23) showcasing phospho-histidine biochemistry and its...