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Egon Willighagen › Comments

Egon Willighagen
Reshared post from Altmetric: - https://plus.google.com/1041867...
Original Post from Altmetric: Who talks about which research? A recent Scientific American visualization examines the differences in what is picked up on by academics vs. the public:  Twitter, mainstream media and academic blogs focus on surprisingly different scientific subjects - Egon Willighagen
Egon Willighagen
Reshared post from Wikidata: - https://plus.google.com/1041867...
Original Post from Wikidata: Want to help out with mapping schema.org and Wikidata properties? Here is the ticket for it: Schema.org should have mappings to Wikidata terms where possible · Issue #280 · schemaorg/schemaorg · GitHub - Egon Willighagen
Egon Willighagen
Time management: Seize the moment - http://www.citeulike.org/user...
Nature, Vol. 517, No. 7535. (21 January 2015), pp. 517-519, doi:10.1038/nj7535-517a Jeffrey Perkel - Egon Willighagen
Egon Willighagen
No paradox, no progress: inverse cancer comorbidity in people with other complex diseases - http://www.citeulike.org/user...
The Lancet Oncology, Vol. 12, No. 6. (June 2011), pp. 604-608, doi:10.1016/s1470-2045(11)70041-9 In the past 5 years, several leading groups have attempted to explain why individuals with Down's syndrome have a reduced risk of many solid tumours and an increased risk of leukaemia and testicular cancer. Niels Bohr, the Danish physicist, noted that a paradox could initiate progress. We think that the paradox of a medical disorder protecting against cancer could be formalised in a new model of inverse cancer morbidity in people with other serious diseases. In this Personal View, we review evidence from epidemiological and clinical studies that supports a consistently lower than expected occurrence of cancer in patients with Down's syndrome, Parkinson's disease, schizophrenia, diabetes, Alzheimer's disease, multiple sclerosis, and anorexia nervosa. Intriguingly, most comorbidities are neuropsychiatric or CNS disorders. We provide a brief overview of evidence indicating genetic and... - Egon Willighagen
Egon Willighagen
eXamine: Exploring annotated modules in networks - http://www.citeulike.org/user...
BMC Bioinformatics, Vol. 15, No. 1. (07 July 2014), 201, doi:10.1186/1471-2105-15-201 Biological networks have a growing importance for the interpretation of high-throughput “omics” data. Integrative network analysis makes use of statistical and combinatorial methods to extract smaller subnetwork modules, and performs enrichment analysis to annotate the modules with ontology terms or other available knowledge. This process results in an annotated module, which retains the original network structure and includes enrichment information as a set system. A major bottleneck is a lack of tools that allow exploring both network structure of extracted modules and its annotations. Kasper Dinkla, Mohammed El-Kebir, Cristina-Iulia Bucur, Marco Siderius, Martine Smit, Michel Westenberg, Gunnar Klau - Egon Willighagen
Egon Willighagen
(21 January 2015), doi:10.6084/m9.figshare.1291646 The passport data from CGN for their genebank (germline/seed) collections of Tomato Frank Menting - Egon Willighagen
Egon Willighagen
Automatically exposing OpenLifeData via SADI semantic Web Services - http://www.citeulike.org/user...
Journal of Biomedical Semantics, Vol. 5, No. 1. (19 November 2014), 46, doi:10.1186/2041-1480-5-46 Two distinct trends are emerging with respect to how data is shared, collected, and analyzed within the bioinformatics community. First, Linked Data, exposed as SPARQL endpoints, promises to make data easier to collect and integrate by moving towards the harmonization of data syntax, descriptive vocabularies, and identifiers, as well as providing a standardized mechanism for data access. Second, Web Services, often linked together into workflows, normalize data access and create transparent, reproducible scientific methodologies that can, in principle, be re-used and customized to suit new scientific questions. Constructing queries that traverse semantically-rich Linked Data requires substantial expertise, yet traditional RESTful or SOAP Web Services cannot adequately describe the content of a SPARQL endpoint. We propose that content-driven Semantic Web Services can enable facile... - Egon Willighagen
Egon Willighagen
Database citation in supplementary data linked to Europe PubMed Central full text biomedical articles - http://www.citeulike.org/user...
Journal of Biomedical Semantics, Vol. 6, No. 1. (05 January 2015), 1, doi:10.1186/2041-1480-6-1 In this study, we present an analysis of data citation practices in full text research articles and their corresponding supplementary data files, made available in the Open Access set of articles from Europe PubMed Central. Our aim is to investigate whether supplementary data files should be considered as a source of information for integrating the literature with biomolecular databases. Åenay Kafkas, Jee-Hyub Kim, Xingjun Pi, Johanna McEntyre - Egon Willighagen
Egon Willighagen
Reshared post from Daniel Mietchen: - https://plus.google.com/1041867...
Original Post from Daniel Mietchen: Here is the final version of our openly drafted research proposal submitted last week to the EU: http://dx.doi.org/10... #Wikidata #opendata #openscience   Wiki4R will create an innovative virtual research environment (VRE) for Open Science at scale, engaging both professional researchers and citizen data scientists in new and potentially transformative forms of collaboration. It is based on the realizations that (1) the structured parts of the Web itself can be regarded as a VRE, (2) such environments depend on communities, (3) closed environments are limited in their capacity to nurture thriving c... - Egon Willighagen
Egon Willighagen
The first eNanoMapper prototype: A substance database to support safe-by-design - http://www.citeulike.org/user...
In Bioinformatics and Biomedicine (BIBM), 2014 IEEE International Conference on (November 2014), pp. 1-9, doi:10.1109/bibm.2014.6999367 Nina Jeliazkova, Philip Doganis, Bengt Fadeel, Roland Grafstrom, Janna Hastings, Vedrin Jeliazkov, Pekka Kohonen, Cristian Munteanu, Haralambos Sarimveis, Bart Smeets, Georgia Tsiliki, David Vorgrimmler, Egon Willighagen - Egon Willighagen
Egon Willighagen
Adapt this general purpose slide deck to share information about ORCID at YOUR organization. - Egon Willighagen
Egon Willighagen
BioModels: ten-year anniversary - http://www.citeulike.org/user...
Nucleic Acids Research, Vol. 43, No. D1. (28 January 2015), pp. D542-D548, doi:10.1093/nar/gku1181 BioModels (http://www.ebi.ac.uk/biomode...) is a repository of mathematical models of biological processes. A large set of models is curated to verify both correspondence to the biological process that the model seeks to represent, and reproducibility of the simulation results as described in the corresponding peer-reviewed publication. Many models submitted to the database are annotated, cross-referencing its components to external resources such as database records, and terms from controlled vocabularies and ontologies. BioModels comprises two main branches: one is composed of models derived from literature, while the second is generated through automated processes. BioModels currently hosts over 1200 models derived directly from the literature, as well as in excess of 140 000 models automatically generated from pathway resources. This represents an approximate 60-fold growth for... - Egon Willighagen
Egon Willighagen
The intriguing relationship between the ABO blood group, cardiovascular disease, and cancer - http://www.citeulike.org/user...
BMC Medicine, Vol. 13, No. 1. (15 January 2015), 7, doi:10.1186/s12916-014-0250-y Other than being present at the surface of red blood cells, the antigens of the ABO blood group system are efficiently expressed by a variety of human cells and tissues. Several studies recently described the involvement of the ABO blood group in the pathogenesis of many human disorders, including cardiovascular disease and cancer, so that its clinical significance extends now beyond the traditional boundaries of transfusion medicine. In a large cohort study recently published in BMC Medicine and including over 50,000 subjects, Etemadi and colleagues reported that nearly 6% of total deaths and as many as 9% of cardiovascular deaths could be attributed to having non-O blood groups, a condition that was also found to be associated with increased risk of gastric cancer. In this commentary, the clinical implications of ABO blood groups are critically discussed and a possible common pathogenic mechanism... - Egon Willighagen
Egon Willighagen
Scientific method: Statistical errors - http://www.citeulike.org/user...
Nature, Vol. 506, No. 7487. (12 February 2014), pp. 150-152, doi:10.1038/506150a P values, the 'gold standard' of statistical validity, are not as reliable as many scientists assume. Regina Nuzzo - Egon Willighagen
Egon Willighagen
Methods of integrating data to uncover genotype-phenotype interactions - http://www.citeulike.org/user...
Nat Rev Genet, Vol. 16, No. 2. (13 February 2015), pp. 85-97, doi:10.1038/nrg3868 Marylyn Ritchie, Emily Holzinger, Ruowang Li, Sarah Pendergrass, Dokyoon Kim - Egon Willighagen
Egon Willighagen
Markus updated the Wikidata-ToolKit to accommodate for the updated HTML download page of JSON dumps. Also, he explained the expected data structure so that I can use the manually downloaded JSON. We... - Egon Willighagen
Egon Willighagen
The neXtProt knowledgebase on human proteins: current status. - http://www.citeulike.org/user...
Nucleic acids research, Vol. 43, No. Database issue. (28 January 2015) neXtProt (http://www.nextprot.org) is a human protein-centric knowledgebase developed at the SIB Swiss Institute of Bioinformatics. Focused solely on human proteins, neXtProt aims to provide a state of the art resource for the representation of human biology by capturing a wide range of data, precise annotations, fully traceable data provenance and a web interface which enables researchers to find and view information in a comprehensive manner. Since the introductory neXtProt publication, significant advances have been made on three main aspects: the representation of proteomics data, an extended representation of human variants and the development of an advanced search capability built around semantic technologies. These changes are presented in the current neXtProt update. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. Pascale Gaudet, Pierre-André Michel, Monique... - Egon Willighagen
Egon Willighagen
Do you want a better understanding of the world around you? Spend one hour with an introductory programming... - https://plus.google.com/1041867...
Do you want a better understanding of the world around you? Spend one hour with an introductory programming course. Best one hour you can invest in yourself today!  The Hour of Code is a global movement reaching tens of millions of students in 180+ countries and over 30 languages. Ages 4 to 104. - Egon Willighagen
Egon Willighagen
So, apparently Elsevier are launching a new open access mega-journal some time this year, joining the bandwagon of similar efforts from almost every other major publisher. A lovely acknowledgement ... - Egon Willighagen
Egon Willighagen
#wikidata   Wikidata Project · Home · Technical 1/1 · Comments 0 · Collections · Download 3.64GB. Type: Dataset Tags: wikidata, json. Bibtex: @misc{, title = {20150112.json.gz}, author = {Wikidata Project}, year = {2015}, license = {CCZero}, abstract = {JSON dump of the Wikidata of 2015-01-12.} } ... - Egon Willighagen
Egon Willighagen
BioTorrents: A File Sharing Service for Scientific Data - http://www.citeulike.org/user...
PLoS ONE, Vol. 5, No. 4. (14 April 2010), e10071, doi:10.1371/journal.pone.0010071 The transfer of scientific data has emerged as a significant challenge, as datasets continue to grow in size and demand for open access sharing increases. Current methods for file transfer do not scale well for large files and can cause long transfer times. In this study we present BioTorrents, a website that allows open access sharing of scientific data and uses the popular BitTorrent peer-to-peer file sharing technology. BioTorrents allows files to be transferred rapidly due to the sharing of bandwidth across multiple institutions and provides more reliable file transfers due to the built-in error checking of the file sharing technology. BioTorrents contains multiple features, including keyword searching, category browsing, RSS feeds, torrent comments, and a discussion forum. BioTorrents is available at http://www.biotorrents.net. Morgan Langille, Jonathan Eisen - Egon Willighagen
Egon Willighagen
BitTorious: global controlled genomics data publication, research and archiving via BitTorrent extensions - http://www.citeulike.org/user...
BMC Bioinformatics, Vol. 15, No. 1. (21 December 2014), 6601, doi:10.1186/s12859-014-0424-9 Centralized silos of genomic data are architecturally easier to initially design, develop and deploy than distributed models. However, as interoperability pains in EHR/EMR, HIE and other collaboration-centric life sciences domains have taught us, the core challenge of networking genomics systems is not in the construction of individual silos, but the interoperability of those deployments in a manner embracing the heterogeneous needs, terms and infrastructure of collaborating parties. This article demonstrates the adaptation of BitTorrent to private collaboration networks in an authenticated, authorized and encrypted manner while retaining the same characteristics of standard BitTorrent. Preston Lee, Valentin Dinu - Egon Willighagen
Egon Willighagen
Research Data Explored: Citations versus Altmetrics - http://www.citeulike.org/user...
(14 Jan 2015) The study explores the citedness of research data, its distribution over time and how it is related to the availability of a DOI (Digital Object Identifier) in Thomson Reuters' DCI (Data Citation Index). We investigate if cited research data "impact" the (social) web, reflected by altmetrics scores, and if there is any relationship between the number of citations and the sum of altmetrics scores from various social media-platforms. Three tools are used to collect and compare altmetrics scores, i.e. PlumX, ImpactStory, and Altmetric.com. In terms of coverage, PlumX is the most helpful altmetrics tool. While research data remain mostly uncited (about 85%), there has been a growing trend in citing data sets published since 2007. Surprisingly, the percentage of the number of cited research data with a DOI in DCI has decreased in the last years. Only nine repositories account for research data with DOIs and two or more citations. The number of cited research data with... - Egon Willighagen
Egon Willighagen
Chemistry of ageing. Edited by: Dr Elizabeth Ostler. Chemistry of Ageing. Gerontology has traditionally been dominated by biological research groups. In recent years, the potential impact of chemical analysis and small molecule interventions has become widely recognised, and there are now a ... - Egon Willighagen
Egon Willighagen
Someone has time to try this for bioinformatics today?? - https://plus.google.com/1041867...
Someone has time to try this for bioinformatics today?? “Playful wikiGraph by @erikabugs visualizes the shortest path between Wikipedia articles: http://t.co/30TjGb4BTv” - Egon Willighagen
Egon Willighagen
Mmm... brain folds are not random and even conserved... French research in PNAS. We have a groovy chimpansees... - https://plus.google.com/1041867...
Mmm... brain folds are not random and even conserved... French research in PNAS. We have a groovy chimpansees don't; the rest of the folds are more or less the same. Mensen hebben een unieke plooi in hun hersenen die mogelijk van pas komt bij taalverwerving. Dat blijkt uit nieuw wetenschappelijk onderzoek. - Egon Willighagen
Egon Willighagen
Nonsteroidal anti-inflammatory drug - http://en.wikipedia.org/w...
Egonw: Undid revision 642045644 by Egonw (talk) {{Use dmy dates|date=July 2012}} [[File:200mg ibuprofen tablets.jpg|thumb|275px|Coated 200 mg tablets of generic [[ibuprofen]], a common NSAID]] '''Nonsteroidal anti-inflammatory drugs''' (usually abbreviated to '''NSAIDs''' {{IPAc-en|ˈ|ɛ|n|s|ɛ|d}} {{respell|EN|sed}}), also called '''nonsteroidal anti-inflammatory agents/analgesics''' ('''NSAIAs''') or '''nonsteroidal anti-inflammatory medicines''' ('''NSAIMs'''), are a class of [[Medication|drug]]s that provides [[analgesic]] (pain-killing) and [[antipyretic]] (fever-reducing) effects, and, in higher doses, [[anti-inflammatory]] effects. The term ''nonsteroidal'' distinguishes these drugs from [[steroids]], which, among a broad range of other effects, have a similar [[eicosanoid]]-depressing, anti-inflammatory action. As analgesics, NSAIDs are unusual in that they are non-[[narcotic]] and thus are used as a non-addictive alternative to narcotics. [[File:NSAID label.jpg|thumb|175px|NSAID... - Egon Willighagen
Egon Willighagen
Nonsteroidal anti-inflammatory drug - http://en.wikipedia.org/w...
Egonw: {{Use dmy dates|date=July 2012}} {{Infobox drug class | Name = Nonsteroidal anti-inflammatory drugs | Image = 200mg ibuprofen tablets.svg | Alt = | Caption = Coated 200 mg tablets of generic [[ibuprofen]], a common NSAID | Use = | Biological_target = | ATC_prefix = | MeshID = | Drugs.com = | Consumer_Reports = | medicinenet = | rxlist = }} '''Nonsteroidal anti-inflammatory drugs''' (usually abbreviated to '''NSAIDs''' {{IPAc-en|ˈ|ɛ|n|s|ɛ|d}} {{respell|EN|sed}}), also called '''nonsteroidal anti-inflammatory agents/analgesics''' ('''NSAIAs''') or '''nonsteroidal anti-inflammatory medicines''' ('''NSAIMs'''), are a class of [[Medication|drug]]s that provides [[analgesic]] (pain-killing) and [[antipyretic]] (fever-reducing) effects, and, in higher doses, [[anti-inflammatory]] effects. The term ''nonsteroidal'' distinguishes these drugs from [[steroids]], which, among a broad range of other effects, have a similar [[eicosanoid]]-depressing, anti-inflammatory action. As analgesics,... - Egon Willighagen
Egon Willighagen
December saw the end of this year's PRA3006 course (aka #mcspils). Time to blog some screenshots of the student projects. Like last year, the aim is to use the Open PHACTS API to collect data with ops.js and which should then... - Egon Willighagen
Egon Willighagen
Programming in the Life Sciences #21: 2014 Screenshots #1 December saw the end of this year's PRA3006... - https://plus.google.com/1041867...
Programming in the Life Sciences #21: 2014 Screenshots #1 December saw the end of this year's PRA3006 course (aka #mcspils ). Time to blog some screenshots of the student projects. Like last year, the aim is to use the Open PHACTS API to collect data with ops.js and which should then be visualized in a HTML page, ... December saw the end of this year's PRA3006 course (aka #mcspils). Time to blog some screenshots of the student projects. Like last year, the aim is to use the Open PHACTS API to collect data with ops.js and which should then... - Egon Willighagen
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