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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
egonw deleted branch feature/compareModels at egonw/bioclipse.rdf - https://github.com/
egonw deleted branch feature/compareModels at egonw/bioclipse.rdf
egonw deleted branch random/versioningAndDeps at egonw/bioclipse.rdf - https://github.com/
egonw deleted branch random/versioningAndDeps at egonw/bioclipse.rdf
egonw pushed to develop at egonw/bioclipse.rdf - https://github.com/egonw...
egonw pushed to develop at egonw/bioclipse.rdf
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
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
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
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
egonw opened issue enanomapper/slimmer#12 - https://github.com/enanoma...
egonw opened issue enanomapper/slimmer#12
CGN tomato passport data - http://www.citeulike.org/user...
(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
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
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
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
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
Adapt this general purpose slide deck to share information about ORCID at YOUR organization. - Egon Willighagen
egonw pushed to master at egonw/citeulike - https://github.com/egonw...
egonw pushed to master at egonw/citeulike
egonw pushed to master at BiGCAT-UM/WikiPathwaysCurator - https://github.com/BiGCAT-...
egonw pushed to master at BiGCAT-UM/WikiPathwaysCurator
egonw pushed to master at BiGCAT-UM/WikiPathwaysCurator - https://github.com/BiGCAT-...
egonw pushed to master at BiGCAT-UM/WikiPathwaysCurator
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
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
egonw pushed to master at BiGCAT-UM/wp2lod - https://github.com/BiGCAT-...
egonw pushed to master at BiGCAT-UM/wp2lod
egonw pushed to master at egonw/wp2lod - https://github.com/egonw...
egonw pushed to master at egonw/wp2lod
egonw pushed to master at BiGCAT-UM/wp2lod - https://github.com/BiGCAT-...
egonw pushed to master at BiGCAT-UM/wp2lod
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
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
egonw pushed to master at BiGCAT-UM/wp2lod - https://github.com/BiGCAT-...
egonw pushed to master at BiGCAT-UM/wp2lod
egonw pushed to master at BiGCAT-UM/wp2lod - https://github.com/BiGCAT-...
egonw pushed to master at BiGCAT-UM/wp2lod
egonw pushed to master at BiGCAT-UM/wp2lod - https://github.com/BiGCAT-...
egonw pushed to master at BiGCAT-UM/wp2lod
egonw pushed to master at BiGCAT-UM/wp2lod - https://github.com/BiGCAT-...
egonw pushed to master at BiGCAT-UM/wp2lod
egonw pushed to master at egonw/wp2lod - https://github.com/egonw...
egonw pushed to master at egonw/wp2lod
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