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Publication Committee Meeting HUPO 5th Annual World Congress Long Beach, CA, USA 30 October 2006

Sandra Orchard, Albert Heck, Mathias Uhlen, Peipei Ping
<span title="">2007</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fuys75pzlrec5izxlpab5g6jue" style="color: black;">Proteomics</a> </i> &nbsp;
Discussions centred on how best to structure interactions between journals, databases and researchers to improve accessibility to data, and facilitate comparisons between datasets.  ...  This meeting brought together delegates from industry, academia and the publishing houses to facilitate discussions on the level of support from the journals for the use of standardised data formats and  ...  All major public domain molecular interaction repositories already export data in this format and MIMIx-compliant data submission tools are publicly available (http://imex.sf.net).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/pmic.200700015">doi:10.1002/pmic.200700015</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17340644">pmid:17340644</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dfkkmhnf3fhuzh2liuzilahspq">fatcat:dfkkmhnf3fhuzh2liuzilahspq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200710114542/https://dspace.library.uu.nl/bitstream/handle/1874/26421/27_hupo_heck.pdf?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/60/e3/60e3a5379d710b4edf16d3029cf8ff98a55876bb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/pmic.200700015"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

Next-Generation Pathology [chapter]

Peter D. Caie, David J. Harrison
<span title="">2016</span> <i title="Springer New York"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6v4flwr6afbfrmhdyu6xe3dyvm" style="color: black;">Msphere</a> </i> &nbsp;
The integration of standardised multi-omics Big-Data and the retention of valuable information on spatial heterogeneity is imperative to model complex disease mechanisms.  ...  The field of pathology is rapidly transforming from a semi-quantitative and empirical science toward a Big-Data discipline.  ...  Clinical and molecular data is now also being integrated with the complex and data-rich image-based phenotypic signatures to investigate cancer heterogeneity and its interaction with the microenvironment  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-4939-3283-2_4">doi:10.1007/978-1-4939-3283-2_4</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26677179">pmid:26677179</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uithnzbsuraetn3y4spt52vqd4">fatcat:uithnzbsuraetn3y4spt52vqd4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190307045528/http://pdfs.semanticscholar.org/d196/742e06d5b401a7efa546ff0d1fb9c0ad3bc5.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d1/96/d196742e06d5b401a7efa546ff0d1fb9c0ad3bc5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-4939-3283-2_4"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Genetic and molecular epidemiology

J. P A Ioannidis
<span title="2007-09-01">2007</span> <i title="BMJ"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfshcwd4hvefvd4pc3aelsy2au" style="color: black;">Journal of Epidemiology and Community Health</a> </i> &nbsp;
However, the pursuit of complex models and interactions has been hampered by small sample sizes and inadequate study design in many molecular applications.  ...  [5] [6] [7] [8] [9] These efforts should be expanded and become more standardised, so as to allow the information to be used by all teams working on specific molecular epidemiology topics. 10 A careful  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1136/jech.2006.059055">doi:10.1136/jech.2006.059055</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17699527">pmid:17699527</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2659995/">pmcid:PMC2659995</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zjsylu57ojdavi3ejxmpko7h54">fatcat:zjsylu57ojdavi3ejxmpko7h54</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170813152529/http://jech.bmj.com/content/jech/61/9/757.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a5/8e/a58e30e3edbc18f8521cb72f7614c10085659840.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1136/jech.2006.059055"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> bmj.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2659995" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination

<span title="2019-10-01">2019</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
We define the new term 'causal interaction', and related child terms, which are children of the PSI-MI 'molecular interaction' term.  ...  Supplementary data are available at Bioinformatics online.  ...  Acknowledgements We thank Birgit Meldal for critically reading and reviewing the manuscript. Funding  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btz132">doi:10.1093/bioinformatics/btz132</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30793173">pmid:30793173</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6896241/">pmcid:PMC6896241</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jgsbahpzwvcatdk2cn4usdyjyi">fatcat:jgsbahpzwvcatdk2cn4usdyjyi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200505083654/https://discovery.ucl.ac.uk/id/eprint/10068977/1/btz132.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ce/41/ce415cf7e34992c50df8bfedb56cb56771e1eeb9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btz132"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6896241" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Projects Exchange 2021: Cross-NCRIS

Julia Martin
<span title="2021-03-03">2021</span> <i title="Zenodo"> Zenodo </i> &nbsp;
These slides present the seven projects from the Cross-NCRIS Data Assets Program, which forms partnerships to aggregate, harmonise and integrate data across national facilities.  ...  Matthew Tucker (APPF) Biomedical Discovery Asset - Dan Andrews (PA) Integrated Microscopy and Proteomics (IMP) - Alex de Marco (EMBL) Australian Urban Health Indicators - Tracy Baylis (AURIN)  ...  standardised assets.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.4642867">doi:10.5281/zenodo.4642867</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kcusggnjenevpnfxvusbi6nsym">fatcat:kcusggnjenevpnfxvusbi6nsym</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210329023654/https://zenodo.org/record/4642867/files/Project%20exchange%202021_NDA_XN_final.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/18/69/18696fae1fe847dc3cdaed41399518c6c1d30461.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.4642867"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> zenodo.org </button> </a>

COSIFER: a python package for the consensus inference of molecular interaction networks

Matteo Manica, Charlotte Bunne, Roland Mathis, Joris Cadow, Mehmet Eren Ahsen, Gustavo A Stolovitzky, María Rodríguez Martínez, Alfonso Valencia
<span title="2020-11-02">2020</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
Here we present COSIFER, a package and a companion web-based platform to infer molecular networks from expression data using state-of-the-art consensus approaches.  ...  Summary The advent of high-throughput technologies has provided researchers with measurements of thousands of molecular entities and enable the investigation of the internal regulatory apparatus of the  ...  This project has received funding from the European Union's Horizon 2020 Research and Innovation Program under grant agreements No 668858 and No 826121.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btaa942">doi:10.1093/bioinformatics/btaa942</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33241320">pmid:33241320</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fqg3sog3kfbahbyzdls4fqbcfe">fatcat:fqg3sog3kfbahbyzdls4fqbcfe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201125043011/https://watermark.silverchair.com/btaa942.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAuAwggLcBgkqhkiG9w0BBwagggLNMIICyQIBADCCAsIGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMFU3s7msx2Y-W12VpAgEQgIICkwdtXZbSyznbxEAvkHcCdwUh2FaWpkCUmvyJncVc4fEMtUuvMmzZcUOKQCEb7qgapvbex8C8x2yMYRaoTT4rvHu9J1ijGLLTJqexuKnrPSfMQz-AG9xigFrq4LLVdSB7MfBu6f4AhQKbKLrY7k0gh1LjmstjIqN260WIGuMFPSJt3mVTQnQpoyeNqO61YdcSW7ED__XUSeA4Ftp9pDie3eVXcL5Q3gHWtWjdhkH5DKeo9k77ZVBh7cXIqO-m5EQL6xUqkfMGiEA9cEL3_LVyTXP3y6Y6T_qGlhDMIgPuINKwJVOVzCL6trFwxS0SG5SA5EJa86A8WnPdWL9AZ_kp3i31RrZHnxCdFsbyPwqx-9GzDeThk4vnKZiRO1P3-HfaBjLVpRWfBvNn5Z6GOXwAjHcmUEd0yAd2Rv2oCiXJSEqvuLZ2Ol_nxCZyDqgZK-9FhP5HUPMZVVXun2Awnf-_Ls14vVGbE7mWLDPhKG4741Uxo9yERMhxauASliBDrV1K5saGz0aEg7wAJZAa0oWsDoBbWhjCYn6Xo18az9tjYlIgyIb9UWyMS8vmHVSQi_Ecy72vF6dH_M43iaYH3roaQmPm2etzOIwYPexq7E8nvHBPDgEmme7wj1JRENhUeBufDxd9T2ro_RpT63L4-Ml4XKI1ZIxIdEv6w9EIAdYVwUWxNSWTwui7TvMsEqgsf63evlYKJ1u7Z1zri5dEUE9Bqm96u9_HdusQUsbtd-GxpM0-STcCDm1ghWr2c7SUyMb-rd4hpBUB2arIf4QX4kxkDnT5-CkFmEveGF4lnLXifUHgt3q1EMn7MMGh5ls6AjNgNI1vSznbiaBsSLRDOiwYnAhBaUUf1LgOoclgPNnoM8i9aBbH" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ef/54/ef549716953834c8acbff77715ffd859bcba4414.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btaa942"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Factor correction as a tool to eliminate between-session variation in replicate experiments: application to molecular biology and retrovirology

Jan M Ruijter, Helene H Thygesen, Onard J L M Schoneveld, Atze T Das, Ben Berkhout, Wouter H Lamers
<span title="2006-01-06">2006</span> <i title="Springer (Biomed Central Ltd.)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rhihhtbynza5veezyszwayabia" style="color: black;">Retrovirology</a> </i> &nbsp;
In normalisation all values in a session are divided by the observed value of the 'control' condition, whereas in standardisation, the sessions' means and standard deviations are used to correct the data  ...  On the contrary, most researchers deal with such between-session variation by normalisation or standardisation of the data.  ...  Fred W. van Leeuwen and Dr. Antoine H.C. van Kampen for their helpful discussions and critical comments during the preparation of this manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1742-4690-3-2">doi:10.1186/1742-4690-3-2</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16398936">pmid:16398936</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1368993/">pmcid:PMC1368993</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3u2gzmur7rchvpexri2q3ug6hu">fatcat:3u2gzmur7rchvpexri2q3ug6hu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190428061400/https://retrovirology.biomedcentral.com/track/pdf/10.1186/1742-4690-3-2" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a0/81/a0816a55936b246200f8519c533534065480c140.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1742-4690-3-2"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1368993" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Standardising Proteomics Data – the W ork of the HUPO Proteomics Standards Initiative

Sandra Orchard, Henning Hermjakob
<span title="2008-04-20">2008</span> <i title="OMICS Publishing Group"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/725mfs2xfzfptd2w2m3qgwelba" style="color: black;">Journal of Proteomics &amp; Bioinformatics</a> </i> &nbsp;
Progress in developing Data Interchange Molecular Interactions The Molecular Interaction workgroup lead the field in publishing and implementing these standards, with Level 1.0 of the XML schema, and  ...  ; to date, protein/peptide separations, mass spectrometry and molecular interactions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4172/jpb.1000002">doi:10.4172/jpb.1000002</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4mq5d3s6qvewlcijpa5d7k5j5m">fatcat:4mq5d3s6qvewlcijpa5d7k5j5m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170813094253/https://www.omicsonline.com/Archive/April2008/JPB1.3.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/2e/32/2e326f1c5cb6b7facccd03729e0122cfd067b4e5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4172/jpb.1000002"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms [article]

Marek Ostaszewski, Anna Niarakis, Alexander Mazein, Inna Kuperstein, Robert Phair, Aurelio Orta-Resendiz, Vidisha Singh, Sara Sadat Aghamiri, Marcio Luis Acencio, Enrico Glaab, Andreas Ruepp, Gisela Fobo (+125 others)
<span title="2020-10-28">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
COVID-19 Disease Map for mechanistic data interpretation and predictions.  ...  We describe the contents of the map and their relevance to the molecular pathophysiology of COVID-19 and the analytical and computational modelling approaches that can be applied to the contents of the  ...  Each of these three languages has a different focus: SBML emphasises standardised representation of the data model underlying molecular interactions, SBGNML provides a standardised graphical representation  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.10.26.356014">doi:10.1101/2020.10.26.356014</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gbxecdcnhbb3jehkhdjxmkdlbq">fatcat:gbxecdcnhbb3jehkhdjxmkdlbq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210717133713/https://www.biorxiv.org/content/biorxiv/early/2021/02/26/2020.10.26.356014.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/93/3b/933b793470540614403da7d37abf5c0cc056bb76.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.10.26.356014"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Mortality over two centuries in large pedigree with familial hypercholesterolaemia: family tree mortality study Commentary: Role of other genes and environment should not be overlooked in monogenic disease

E. J G Sijbrands
<span title="2001-04-28">2001</span> <i title="BMJ"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/xl3flnwhiretnie6tm4qjkvr3a" style="color: black;">BMJ (Clinical Research Edition)</a> </i> &nbsp;
This large variability over time and between branches of the pedigree points to a strong interaction with environmental factors.  ...  Mortality was not increased in carriers of the mutation during the 19th and early 20th century; it rose after 1915, reached its maximum between 1935 and 1964 (standardised mortality ratio 1.78, 95% confidence  ...  JCD collected the data, performed the molecular work, and participated in editing and revising the manuscript. PHEMDM performed genealogical research and participated in revising the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1136/bmj.322.7293.1019">doi:10.1136/bmj.322.7293.1019</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/11325764">pmid:11325764</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC31037/">pmcid:PMC31037</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/m4ss5ndiyzbvlhvecrmw5sbceq">fatcat:m4ss5ndiyzbvlhvecrmw5sbceq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170814132248/http://www.bmj.com/content/bmj/322/7293/1019.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/41/fa/41face5a2c3c641d73d6aeb17cc26b1d77d42d8f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1136/bmj.322.7293.1019"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> bmj.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC31037" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Towards Increased Reliability, Transparency and Accessibility in Crosslinking Mass Spectrometry [article]

Alexander Leitner, Alexandre M.J.J. Bonvin, Christoph H. Borchers, Robert J. Chalkley, Julia Chamot-Rooke, Colin W. Combe, Jürgen Cox, Meng-Qiu Dong, Lutz Fischer, Michael Götze, Fabio C. Gozzo, Albert J. R. Heck (+24 others)
<span title="2020-07-01">2020</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
mapping protein interactions in complex mixtures.  ...  Crosslinking MS has become a much-appreciated and routinely applied tool especially in structural biology.  ...  Author contributions Writing -Original draft, A.L. and J.R., Writing -Review and Editing, all authors. Declaration of Interests The authors declare no competing interests.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2007.00383v1">arXiv:2007.00383v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cchlu3nykjcobhydrmfjrwyrqi">fatcat:cchlu3nykjcobhydrmfjrwyrqi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200710055513/https://arxiv.org/ftp/arxiv/papers/2007/2007.00383.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2007.00383v1" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

ExCAPE-DB: an integrated large scale dataset facilitating Big Data analysis in chemogenomics

Jiangming Sun, Nina Jeliazkova, Vladimir Chupakhin, Jose-Felipe Golib-Dzib, Ola Engkvist, Lars Carlsson, Jörg Wegner, Hugo Ceulemans, Ivan Georgiev, Vedrin Jeliazkov, Nikolay Kochev, Thomas J. Ashby (+1 others)
<span title="2017-03-07">2017</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5aubiwi6v5beng6iqzj577kiaa" style="color: black;">Journal of Cheminformatics</a> </i> &nbsp;
This dataset comprises over 70 million SAR data points from publicly available databases (PubChem and ChEMBL) including structure, target information and activity annotations.  ...  Chemogenomics data generally refers to the activity data of chemical compounds on an array of protein targets and represents an important source of information for building in silico target prediction  ...  Availability of data and materials Interactive access as well as download links of user selected subsets or the entire dataset are available at https://solr.ideaconsult.net/search/excape/.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13321-017-0203-5">doi:10.1186/s13321-017-0203-5</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28316655">pmid:28316655</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5340785/">pmcid:PMC5340785</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tqianrarpbbhxcmokicumpialq">fatcat:tqianrarpbbhxcmokicumpialq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171114103259/http://publisher-connector.core.ac.uk/resourcesync/data/Springer-OA/pdf/e95/aHR0cDovL2xpbmsuc3ByaW5nZXIuY29tLzEwLjExODYvczEzMzIxLTAxNy0wMjAzLTUucGRm.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/89/92/8992e843c7411645c8e7517f176828c564fdeb78.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13321-017-0203-5"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5340785" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

An intrinsically disordered proteins community for ELIXIR

Norman E. Davey, M. Madan Babu, Martin Blackledge, Alan Bridge, Salvador Capella-Gutierrez, Zsuzsanna Dosztanyi, Rachel Drysdale, Richard J. Edwards, Arne Elofsson, Isabella C. Felli, Toby J. Gibson, Aleksandras Gutmanas (+32 others)
<span title="2019-10-15">2019</span> <i title="F1000 Research Ltd"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lz7xw3k77zcg5f66jhfurufu64" style="color: black;">F1000Research</a> </i> &nbsp;
and dissemination; integration of IDP data into the ELIXIR Core Data Resources; and the creation of benchmarking criteria for IDP-related software.  ...  The workshop, and further consultation with the members of the wider IDP community, identified the key priority areas for the roadmap including the development of standards for data annotation, storage  ...  For functional data describing protein interactions, molecular interaction interchange standards based on the guidelines of the HUPO-PSI-MI molecular standards (Sivade Dumousseau et al., 2018) can be  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.12688/f1000research.20136.1">doi:10.12688/f1000research.20136.1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31824649">pmid:31824649</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6880265/">pmcid:PMC6880265</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2rw2z5q3obgrllxjcthcqgoiyu">fatcat:2rw2z5q3obgrllxjcthcqgoiyu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210716205636/https://repositori.upf.edu/bitstream/handle/10230/43967/Davey_F1000_intr.pdf;jsessionid=A7C04BD9ED7A2A99C0EA4232B3C8EA25?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d5/ea/d5ea3713a94b2d93d6c85b0ef96072b4dc4f8789.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.12688/f1000research.20136.1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6880265" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

PsicquicGraph, a BioJS component to visualize molecular interactions from PSICQUIC servers

Jose M. Villaveces, Rafael C. Jimenez, Bianca H. Habermann
<span title="2014-02-13">2014</span> <i title="F1000 Research, Ltd."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lz7xw3k77zcg5f66jhfurufu64" style="color: black;">F1000Research</a> </i> &nbsp;
Protein interaction networks have become an essential tool in large-scale data analysis, integration, and the visualization of high-throughput data in the context of complex cellular networks.  ...  Here we introduce PsicquicGraph, an open-source, web-based visualization component for molecular interactions from PSIQUIC services.  ...  For example IntAct, an open-source, open data molecular interaction database 1 contains approximately 275 000 curated binary interactions extracted from over 5000 publications.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.12688/f1000research.3-44.v1">doi:10.12688/f1000research.3-44.v1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25075287">pmid:25075287</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4097353/">pmcid:PMC4097353</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hpq6pbjoyfbfpmdbtkdljry3gm">fatcat:hpq6pbjoyfbfpmdbtkdljry3gm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180722010147/https://f1000researchdata.s3.amazonaws.com/manuscripts/3697/aebe20c5-4809-49c1-8e2b-b01e57511375_3452%20-%20jose%20villaveces.pdf?doi=10.12688/f1000research.3-44.v1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/49/f1/49f1ead190a3df6c44aee3199e7c7343f0755bcf.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.12688/f1000research.3-44.v1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4097353" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Animal models for arthritis: innovative tools for prevention and treatment

G. Kollias, P. Papadaki, F. Apparailly, M. J. Vervoordeldonk, R. Holmdahl, V. Baumans, C. Desaintes, J. Di Santo, J. Distler, P. Garside, M. Hegen, T. W. J. Huizinga (+11 others)
<span title="2011-05-30">2011</span> <i title="BMJ"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/7vfiq4giqbf5lazxvrwe5svawe" style="color: black;">Annals of the Rheumatic Diseases</a> </i> &nbsp;
Effi cient integration and dissemination of information and resources as well as outreach to the public will be necessary to manage the plethora of data accumulated and to increase community awareness  ...  This requires full and standardised characterisation of all models at the genotypic, phenotypic and biomarker level, exploiting recent technological developments in '-omics' profi ling and computational  ...  It is therefore important to create relational databases in which phenotypic, molecular profi ling and clinical data from animal models and patients will be deposited and processed in a systematic and  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1136/ard.2010.148551">doi:10.1136/ard.2010.148551</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21628308">pmid:21628308</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rr3slmcmnzdyzmax7btwtlo2re">fatcat:rr3slmcmnzdyzmax7btwtlo2re</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190304173425/http://pdfs.semanticscholar.org/c0ea/94484f8df40100a13d0d8a03887f76ec2305.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c0/ea/c0ea94484f8df40100a13d0d8a03887f76ec2305.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1136/ard.2010.148551"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> bmj.org </button> </a>
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