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A directory of tools, AI models, datasets, and research resources for biotech, bioinformatics, and other scientific fields. Aggregated from curated GitHub awesome-lists, HuggingFace, bio.tools, Bioconductor, and more.
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20 of 7,064 resources
EMMO is a multidisciplinary effort to develop a standard representational framework (the ontology) for applied sciences. It is based on physics, analytical philosophy and information and communication technologies. It has been instigated by materials science to provide a framework for knowledge capture that is consistent with scientific principles and methodologies. (from GitHub)
The primary goal of this ontology is to standardize the representation of molecular simulation data, processes, and methodologies across disparate simulation platforms, engines (e.g., GROMACS, AMBER, NAMD), and analysis tools, while ensuring these terms are interoperable with existing life sciences ontologies
An ontology with predicates to formalization of the concept of mentions. The mentions may be either explicit (e.g. as when well stated into an article "Dr. Johnson's groundbreaking research on climate change") or implicit (e.g. such as discussing "seminal studies in the field"). MiTO contains the object property mito:mentions and its inverse mito:isMentionedBy.
An EMMO-based domain ontology for atomistic and electronic modelling.
An ontology that provides a structured vocabulary for rhetorical elements within documents (e.g., Introduction, Discussion, Acknowledgements, Reference List, Figures, Appendix). It is imported by DoCO.
An ontology that allows the description of numerical and categorical bibliometric data (e.g., journal impact factor, author h-index, categories describing research careers) in RDF.
The Essential FRBR in OWL2 DL Ontology (FRBR) is an expression in OWL 2 DL of the basic concepts and relations described in the IFLA report on the Functional Requirements for Bibliographic Records (FRBR), also described in Ian Davis's RDF vocabulary. It is imported by FaBiO and BiRO.
An ontology written in OWL 2 DL to enable characterization of the five attributes of an online journal article - peer review, open access, enriched content, available datasets and machine-readable metadata.
An ontology based on PRO for describing the contributions that may be made, and the roles that may be held by a person with respect to a journal article or other publication (e.g. the role of article guarantor or illustrator).
An ontology for describing the steps in the workflow associated with the publication of a document or other publication entity.
METPO (Microbial Ecophysiological Trait and Phenotype Ontology) provides standardized terms for describing microbial phenotypes, growth characteristics, and culture conditions. It includes classes for growth media, temperature tolerances, pH tolerances, and relationships like "grows in" and "does not grow in".
An ontology that permits the number of in-text citations of a cited source to be recorded, together with their textual citation contexts, along with the number of citations a cited entity has received globally on a particular date.
An ontology meant to define bibliographic records, bibliographic references, and their compilation into bibliographic collections and bibliographic lists, respectively.
An ontology that provides a structured vocabulary written of document components, both structural (e.g., block, inline, paragraph, section, chapter) and rhetorical (e.g., introduction, discussion, acknowledgements, reference list, figure, appendix).
An ontology that enables characterization of the nature or type of citations, both factually and rhetorically.
An interactive platform that performs statistical analyses on metabolomics datasets and allows visualising results with ease. The interface gives users autonomy in creating figures suited to their reporting and publication needs.
The Graphic Descriptor Ontology (GDO) is intended for use in describing graphics that represent the form of objects. It uses the language of visual communication, illustration, and technical drawing. The GDO is rooted in the Basic Formal Ontology (BFO) and uses several classes from the Information Entity Ontology of the Common Core Ontologies as a mid-level ontology. [from https://gdo.endlessforms.info/about]
A crystallography domain ontology based on EMMO and the CIF core dictionary. It is implemented as a formal language. (from https://nfdi4cat.org/services/ontologie-sammlung/)