A5048705669- Biomedical Text Mining and Ontologies
- Semantic Web and Ontologies
- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- Wikis in Education and Collaboration
- Genetics, Bioinformatics, and Biomedical Research
- Research Data Management Practices
- Scientific Computing and Data Management
- Natural Language Processing Techniques
- Biomedical and Engineering Education
- Data Quality and Management
- Computational Drug Discovery Methods
- Species Distribution and Climate Change
- Microbial Natural Products and Biosynthesis
- Artificial Intelligence in Healthcare and Education
- Microbial Metabolic Engineering and Bioproduction
- Gene expression and cancer classification
- RNA and protein synthesis mechanisms
- Metabolomics and Mass Spectrometry Studies
- RNA modifications and cancer
- Advanced Database Systems and Queries
- CRISPR and Genetic Engineering
- Genomics and Rare Diseases
- Image Processing and 3D Reconstruction
- Open Source Software Innovations
Diabetes Australia
2024
Terumo (Belgium)
2015-2023
Maastricht University
2011-2023
University of Kansas
2021
Seattle University
2021
Natural History Museum
2021
Bavarian Natural History Collections
2021
Cardiff University
2021
Harvard University
2021
Musée National d'Histoire Naturelle
2021
There is an urgent need to improve the infrastructure supporting reuse of scholarly data. A diverse set stakeholders-representing academia, industry, funding agencies, and publishers-have come together design jointly endorse a concise measureable principles that we refer as FAIR Data Principles. The intent these may act guideline for those wishing enhance reusability their data holdings. Distinct from peer initiatives focus on human scholar, Principles put specific emphasis enhancing ability...
WikiPathways (wikipathways.org) captures the collective knowledge represented in biological pathways. By providing a database curated, machine readable way, omics data analysis and visualization is enabled. other pathway databases are used to analyze experimental by research groups many fields. Due open collaborative nature of platform, our content keeps growing getting more accurate, making reliable rich database. Previously, however, focus was primarily on genes proteins, leaving...
Abstract WikiPathways (https://www.wikipathways.org) is a biological pathway database known for its collaborative nature and open science approaches. With the core idea of scientific community developing curating knowledge in models, lowers all barriers accessing using content. Increasingly more content creators, initiatives, projects tools have started WikiPathways. Central this growth increased use are various communities that focus on particular subsets molecular pathways such as rare...
WikiPathways (http://www.wikipathways.org) is an open, collaborative platform for capturing and disseminating models of biological pathways data visualization analysis. Since our last NAR update, 4 years ago, has experienced massive growth in content, which continues to be contributed by hundreds individuals each year. New aspects the diversity depth collected are described from perspective researchers interested using pathway information their studies. We provide updates on extensions...
The FAIR principles have been widely cited, endorsed and adopted by a broad range of stakeholders since their publication in 2016. By intention, the 15 guiding do not dictate specific technological implementations, but provide guidance for improving Findability, Accessibility, Interoperability Reusability digital resources. This has likely contributed to adoption principles, because individual stakeholder communities can implement own solutions. However, it also resulted inconsistent...
WikiPathways (wikipathways.org) is an open-source biological pathway database. Collaboration and open science are pivotal to the success of WikiPathways. Here we highlight continuing efforts supporting WikiPathways, content growth collaboration among researchers. As evolving database, there a growing need for address overcome technical challenges. In this direction, has undergone major restructuring, enabling renewed approach sharing curating knowledge, thus providing stability future...
Wikidata is a community-maintained knowledge base that has been assembled from repositories in the fields of genomics, proteomics, genetic variants, pathways, chemical compounds, and diseases, adheres to FAIR principles findability, accessibility, interoperability reusability. Here we describe breadth depth biomedical contained within Wikidata, discuss open-source tools have built add information synchronize it with source databases. We also demonstrate several use cases for including...
Making data available as Linked Data using Resource Description Framework (RDF) promotes integration with other web resources. RDF documents can natively link to related data, and others back Uniform Identifiers (URIs). makes the machine-readable uses extensible vocabularies for additional information, making it easier scale up inference analysis.This paper describes recent developments in an ongoing project converting from ChEMBL database into triples. Relative earlier versions, this...
The discovery of new medicines requires pharmacologists to interact with a number information sources ranging from tabular data scientific papers, and other specialized formats. In this application report, we describe linked platform for
The Complex Portal (www.ebi.ac.uk/complexportal) is a manually curated, encyclopaedic database of macromolecular complexes with known function from range model organisms. It summarizes complex composition, topology and along links to large domain-specific resources (i.e. wwPDB, EMDB Reactome). Since the last update in 2019, we have produced first draft complexome for Escherichia coli, maintained updated that Saccharomyces cerevisiae, added over 40 coronavirus increased human 1100 include...
Open biological data are distributed over many resources making them challenging to integrate, update and disseminate quickly. Wikidata is a growing, open community database which can serve this purpose also provides tight integration with Wikipedia. In order improve the state of data, facilitate management dissemination, we imported all human mouse genes, proteins into Wikidata. total, 59 721 genes 73 355 have been from NCBI 27 306 16 728 Swissprot subset UniProt. As be edited by anybody,...
During BioHackathon 24 in Fukushima, we organized a WikiBlitz, collaborative effort to integrate biodiversity observations from iNaturalist into the Wikimedia ecosystem. A WikiBlitz is inspired by concept of BioBlitz, where participants document as many species possible within limited time frame, while also contributing structured data Wikidata, Commons, and Wikipedia. In this report, describe methodology outcomes event, including collection 109 their subsequent verification integration...
The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their data. semantic web standard facilitate knowledge integration using statements built as triples describing relation between two objects. WikiPathways, an collaborative pathway resource, is now available the through SPARQL endpoint at http://sparql.wikipathways.org. Having pathways allows rapid with from other that contain information about...
With the advancement of genome-sequencing technologies, new genomes are being sequenced daily. Although these sequences deposited in publicly available data warehouses, their functional and genomic annotations (beyond genes which predicted automatically) mostly reside text primary publications. Professional curators hard at work extracting those from literature for most studied organisms depositing them structured databases. However, resources don't exist to fund comprehensive curation...
Integration of open access, curated, high-quality information from multiple disciplines in the Life and Biomedical Sciences provides a holistic understanding domain. Additionally, effective linking diverse data sources can unearth hidden relationships guide potential research strategies. However, given lack consistency between descriptors identifiers used different resources absence simple mechanism to link them, gathering combining relevant, comprehensive databases remains challenge. The...
Abstract Wikidata is an open, Semantic Web-compatible database that anyone can edit. This ‘data commons’ provides structured data for Wikipedia articles and other applications. Every article on has a hyperlink to editable item in this database. unique connection the world’s largest community of volunteer knowledge editors could help make key hub within greater Web. The life sciences, as ever, faces crucial challenges disseminating integrating knowledge. Our group addressing these issues by...
Pandemics, even more than other medical problems, require swift integration of knowledge. When caused by a new virus, understanding the underlying biology may help finding solutions. In setting where there are large number loosely related projects and initiatives, we need common ground, also known as "commons." Wikidata, public knowledge graph aligned with Wikipedia, is such commons uses unique identifiers to link in bases. However, Wikidata not always have right schema for urgent questions....
This article acts as a successor to the 10 simple rules for editing Wikipedia from decade ago [1].It addresses Wikipedia's machine-readable cousin: Wikidata-a project potentially even more relevant point of view Computational Biology.Wikidata is free collaborative knowledgebase [2] providing structured data every page and beyond.It relies on same peer production principle Wikipedia: anyone can contribute.Open, models often surprise in how productively they work practice, given unlikely might...
Natural language understanding systems have to exploit various kinds of knowledge in order represent the meaning behind texts. Getting this place is often such a huge enterprise that it tempting look for can discover automatically. We describe how distinction between conceptual and linguistic semantics may assist reaching objective, provided distinguishing them not done too rigorously. present several examples support view argue multilingual environment, ontologies should be designed as...