--- author: - contributor_roles: [] family: Edmunds given: Scott url: https://orcid.org/0000-0001-6444-1436 blog: authors: null community_id: 52db0518-e228-4260-8c54-c4e323b2569d created: 1675555200 current_feed_url: null description: Data driven blogging from the GigaScience editors doi: https://doi.org/10.59350/gigablog favicon: https://rogue-scholar.org/api/communities/52db0518-e228-4260-8c54-c4e323b2569d/logo feed_format: application/atom+xml feed_url: http://gigasciencejournal.com/blog/feed/atom/ filter: null generator: Other home_page_url: https://gigasciencejournal.com/blog issn: null language: eng license: https://creativecommons.org/licenses/by/4.0/legalcode prefix: '10.59350' relative_url: null secure: false slug: gigablog status: archived subfield: '1311' title: GigaBlog updated: null use_api: null container: GigaBlog date: '2011-09-13T00:00:00+00:00' date_updated: '2025-12-06T10:49:33+00:00' guid: http://finaloriginalblogs.dev/gigablog/2011/09/13/hupo-2011-lessons-for-proteomics-from-the-genomics-tsunami/ identifier: https://doi.org/10.59350/vsqx9-txm96 image: http://gigasciencejournal.com/blog/wp-content/uploads/2011/09/hupo_world20111-300x127.jpg images: - height: '127' src: http://gigasciencejournal.com/blog/wp-content/uploads/2011/09/hupo_world20111-300x127.jpg width: '300' - src: http://gigasciencejournal.com/blog/wp-content/uploads/2011/09/hupo_world20111.jpg issn: null keywords: - Health - Conferences - Data - HUPO - Open Data lang: en license: https://creativecommons.org/licenses/by/4.0/legalcode rid: 4avbm-z0e70 rights: https://creativecommons.org/licenses/by/4.0/legalcode summary: Our whistlestop summer conference tour circumnavigating the globe has come to a jetlagged end, with the final conference being last weeks HUPO (Human Proteomics Organisation) congress in Geneva. title: 'HUPO 2011: lessons for Proteomics from the Genomics Tsunami' url: https://wayback.archive-it.org/22098/2025-05-01T17:13:42Z/http://gigasciencejournal.com/blog/hupo-2011-lessons-for-proteomics-from-the-genomics-tsunami version: v1 --- [![](http://gigasciencejournal.com/blog/wp-content/uploads/2011/09/hupo_world20111-300x127.jpg){.alignleft .size-medium .wp-image-654 decoding="async" width="300" height="127"}](http://gigasciencejournal.com/blog/wp-content/uploads/2011/09/hupo_world20111.jpg)Our whistlestop summer conference [tour](http://blogs.biomedcentral.com/gigablog/2011/09/further_adventures_on_the_road "gigascience on the road"){target="_blank" rel="noopener"} circumnavigating the globe has come to a jetlagged end, with the final conference being last weeks HUPO ([Human Proteomics Organisation](http://www.hupo.org/ "HUPO homepage"){target="_blank" rel="noopener"}) [congress](http://www.hupo2011.com/ "HUPO congress 2011"){target="_blank" rel="noopener"} in Geneva. With it being the 10th anniversary meeting it was a good opportunity to look back on how Proteomics has progressed over the [past decade](http://www.nature.com/ng/journal/v33/n3s/full/ng1106.html "Nature Genetics - Proteomics: the first decade and beyond"){target="_blank" rel="noopener"}, from it\'s early gel-based origins to its current more mass-spectrometry based incarnation as a key high-throughput \"Omics\" technology. Whilst there have been huge challenges and some [criticism](http://blog.dannynavarro.net/2010/07/31/sharing-proteomics-data-trickier-than-it-seems/ "sharing proteomics data trickier than it seems"){target="_blank" rel="noopener"} relating to issues with reproducibility (leading even to a \"[fix-proteomics](http://www.fixingproteomics.org/ "Fix proteomics"){target="_blank" rel="noopener"}\" campaign), the several sessions relating to standards, data and repositories were good opportunities to observe how these are currently being addressed. The many talks from members of [HUPO-PSI](http://www.psidev.info/ "HUPO-PSI"){target="_blank" rel="noopener"} (Proteomics Standards Initiative), including four from our editorial board member [Henning Hermjakob](http://www.ebi.ac.uk/Information/Staff/person_maintx.php?person_id=233 "Henning Hermjakob"){target="_blank" rel="noopener"}, demonstrated how organized the community has been to systematically divide up and produce standards, formats, tools and repositories for a diverse range of data types. The HUPO-PSI Initiative Program session followed the full pectrum, from 2D-gels (Juan Pablo Albar presenting on his recent [*BMC Research Notes*](http://www.biomedcentral.com/bmcresnotes/ "BMC Res Notes"){target="_blank" rel="noopener"} [paper](best%20practice%20for%20data%20sharing%20in%20proteomics "http://www.biomedcentral.com/series/datasharing"){target="_blank" rel="noopener"} on best practice for data sharing in  Proteomics) to Molecular Interaction data (Sandra Orchard presenting on the [IMEx consortium](http://www.imexconsortium.org/ "IMEx consortium"){target="_blank" rel="noopener"}). Many of the biggest challenges seemed to be economic and cultural rather than technical, with much discussion on the closing of [Peptidome](http://www.ncbi.nlm.nih.gov/peptidome "Peptidome"){target="_blank" rel="noopener"} by NCBI, and recent stability issues at the main [ProteomExchange](http://www.proteomexchange.org/ "ProteomeExchange"){target="_blank" rel="noopener"} raw data portal -- [Tranche](https://proteomecommons.org/tranche/ "Tranche"){target="_blank" rel="noopener"}. Whilst this is unfortunate, there seemed to be much work in process to rectify issues with raw data hosting, and processed and annotated data seemed to be in safe hands with the [PRIDE](http://www.ebi.ac.uk/pride/ "PRIDE"){target="_blank" rel="noopener"} and [PeptideAtlas](http://www.peptideatlas.org/ "PeptideAtlas"){target="_blank" rel="noopener"} repositories. Whilst adoption and journal compliance is still building up (for an example see our last GigaBlog [posting](http://blogs.biomedcentral.com/gigablog/2011/09/exercises_in_blogging_at_science "Show me the data!"){target="_blank" rel="noopener"}), PRIDE in particular offers authors and reviewers great visualization and quality  assessment tools ([PRIDEInspector](http://code.google.com/p/pride-toolsuite/wiki/PRIDEInspector "PRIDEInspector"){target="_blank" rel="noopener"}), and in light of this our [editorial policies](http://www.gigasciencejournal.com/about#editorialpolicies "Editorial Policies"){target="_blank" rel="noopener"} strongly recommend deposition of suitable data in this database. With a [9-year](http://www.sciencemag.org/cgi/content/summary/296/5569/827?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&searchid=1027414274815_1591&stored_search=&FIRSTINDEX=0&volume=296&firstpage=827&fdate=10/1/1995&tdate=7/31/2002 "HUPO-PSI original paper"){target="_blank" rel="noopener"} history and over 50-[publications](http://www.psidev.info/index.php?q=node/93 "HUPO-PSI pubs"){target="_blank" rel="noopener"} and white-papers produced to date, [HUPO-PSI](http://www.psidev.info/ "HUPO-PSI"){target="_blank" rel="noopener"} has tried to follow many of the lessons learned by Proteomics slightly older \"big-brother\" the Genomics community. With this subject in mind [*GigaScience*](http://www.gigasciencejournal.com "GigaScience journal"){target="_blank" rel="noopener"} presented a talk at the \"Proteomics Repositories and Journals -- a partnership made in heaven/hell?\" session specifically focusing on lessons learned for the Proteomics community from the Genomics \"Tsunami\" (slides [here](http://www.slideshare.net/GigaScience/scott-edmunds-gigascience-a-journal-or-a-database-lessons-learned-from-the-genomics-tsunami "GigaSlides"){target="_blank" rel="noopener"}). Whilst  Proteomics data-volumes are still smaller than the petabytes that the genomics community are currently [struggling](http://www.isgtw.org/feature/knowing-me-knowing-you "Genomics data-problems"){target="_blank" rel="noopener"} with, it\'s reassuring that the growing Proteomics community are trying to preempt these issues. There were interesting talks on show demonstrating very \"genomics-esque\" cloud-based workflow systems such as ISB\'s [TPP](http://www.proteomecenter.org/software.php "TPP"){target="_blank" rel="noopener"} (transproteomic pipeline) amztpp command line tool. It was also interesting to see areas the two fields are coalescing, with [Mike Snyder](http://snyderlab.stanford.edu/ "Snyder Lab"){target="_blank" rel="noopener"} presenting a fantastic personalized-medicine oriented multi-\"Omics\" talk on what he terms *Whole \"Omics\" Profiling* (and BGI calls \"[*Trans-Omics*](http://www.bgisequence.com/home/newsandevents/news/cuhk-bgi-innovation-institute-of-trans-omics-inaugurates-today-a "BGI "){transomics\"\"=\"\" target=\"\_blank\" rel=\"noopener\"}\"). Whilst there are obviously huge challenges that lie ahead, it is clear Proteomics has come a long way in the last decade, and as a key part of the scope of  [*GigaScience*](http://www.gigasciencejournal.com "Gigascience"){target="_blank" rel="noopener"} we hope to be there to cover much of what will progress as the field matures in the decades to come. Please contact us at if you have Proteomics data related research, reviews and comment you would like us to [consider](http://www.gigasciencejournal.com/manuscript "submission system"){target="_blank" rel="noopener"} for the journal. Looking  forward to meeting many of you at [HUPO 2012](http://www.hupo2012.org/ "HUPO 2012"){target="_blank" rel="noopener"} in Boston! The post [HUPO 2011: lessons for Proteomics from the Genomics Tsunami](http://gigasciencejournal.com/blog/hupo-2011-lessons-for-proteomics-from-the-genomics-tsunami/){rel="nofollow"} appeared first on [GigaBlog](http://gigasciencejournal.com/blog){rel="nofollow"}.