cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25504/fairsharing.rdhnqx
title: FAIRsharing record for: BioSimulators conventions for the inputs, outputs, and capabilities of biosimulation software tools
title: BioSimulators conventions

description: This FAIRsharing record describes:  The BioSimulators conventions encompass several conventions for biosimulation tools (see below). In combination with modeling languages such as Cell-ML and SBML, SED-ML, KISAO, and COMBINE/OMEX, the BioSimulators standards enable investigators to use compliant biosimulation tools to execute simulations with the same syntax and generate consistent results. (a) A format for describing the specifications of a biosimulation tool including its name and version; a description of the tool; the modeling frameworks (e.g., logical, constraint-based, kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats (e.g., BNGL, SBML) that the tool supports; the parameters of each algorithm, their data types, and their default values; links to the tool and documentation about the tool; and additional metadata such as citations for the tool.  (b) Specifications for the syntax and semantics of the inputs (command-line arguments) and outputs (reports and charts of simulation results) of command-line interfaces for biosimulation tools. (c) Specifications for (i) the entry points of Docker images of biosimulation tools and (ii) using Docker labels to annotate basic metadata about images such as the name and version of the simulation tool inside the image. (d) A format for describing reports of simulation results, including the numerical predictions, as well as metadata about the semantic meaning of each axis and each individual row and column.
description: The source of this description is the metadata record on FAIRsharing.org, an educational and informative resource that describes and links databases, standards, and data policies. FAIRsharing also creates collections of these resources and recommendations of databases and standards based on 3rd party data policies.
DOI: 10.25504/fairsharing.0b7e54
title: FAIRsharing record for: Handle
title: hdl

description: This FAIRsharing record describes:  The Handle System is the Corporation for National Research Initiatives's proprietary registry assigning persistent identifiers, or handles, to information resources, and for resolving "those handles into the information necessary to locate, access, and otherwise make use of the resources". As with handles used elsewhere in computing, Handle System handles are opaque, and encode no information about the underlying resource, being bound only to metadata regarding the resource. Consequently, the handles are not rendered invalid by changes to the metadata.
description: The source of this description is the metadata record on FAIRsharing.org, an educational and informative resource that describes and links databases, standards, and data policies. FAIRsharing also creates collections of these resources and recommendations of databases and standards based on 3rd party data policies.
DOI: 10.15468/dl.t6ebxt
title: Occurrence Download

description: A dataset containing 8717 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tsuga canadensis (L.) Carrière",
 "Geometry POLYGON((-105 38, -80 38, -80 58, -105 58, -105 38))"
 ]
}

 The dataset includes 8717 records from 58 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020630-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25504/fairsharing.3ccrpf
title: FAIRsharing record for: PyNN
title: PyNN

description: This FAIRsharing record describes:  The PyNN API aims to support modelling at a high-level of abstraction (populations of neurons, layers, columns and the connections between them) while still allowing access to the details of individual neurons and synapses when required. PyNN provides a library of standard neuron, synapse and synaptic plasticity models, which have been verified to work the same on the different supported simulators. PyNN also provides a set of commonly-used connectivity algorithms (e.g. all-to-all, random, distance-dependent, small-world) but makes it easy to provide your own connectivity in a simulator-independent way, either using the Connection Set Algebra or by writing your own Python code. PyNN has been developed as a procedural description in Python which can be used to instantiate a network across multiple simulators.
description: The source of this description is the metadata record on FAIRsharing.org, an educational and informative resource that describes and links databases, standards, and data policies. FAIRsharing also creates collections of these resources and recommendations of databases and standards based on 3rd party data policies.
DOI: 10.25504/fairsharing.e0b3b3
title: FAIRsharing record for: FAIR chemical structure template
title: null

description: This FAIRsharing record describes:  Open specification that describes how chemical structures in journal articles can be shared in a FAIR way.
description: The source of this description is the metadata record on FAIRsharing.org, an educational and informative resource that describes and links databases, standards, and data policies. FAIRsharing also creates collections of these resources and recommendations of databases and standards based on 3rd party data policies.
DOI: 10.25504/fairsharing.pqzyd5
title: FAIRsharing record for: MultiCellular Data Standard
title: MultiCellDS

description: This FAIRsharing record describes:  MultiCellDS (Multicellular data specification), an outgrowth of the earlier MultiCellXML project, aims to create a data standard for sharing multicellular experimental, simulation, and clinical data. Our ultimate goal is to foster a community that develops user-friendly tools that can read, write, and recombine data into better simulations and analyses for multicellular biology and predictive medicine. As part of this effort, we are developing MultiCellDB: a repository for a curated library of digital cell lines and peer-reviewed simulation and experimental data. A novel part of MultiCellDS is the digital cell line: a digital analogue of experimental cell lines that will help to collect biophysical cell line measurements coming from many research groups and make them readily accessible to an ecosystem of compatible computational models. You can learn more about digital cell lines and other core ideas on this page. We are currently preparing a draft of the upcoming MultiCellDS 1.0 specification. After a multiple rounds of comment and review by a multidisciplinary review panel and the general public, we target an October 2016 release of the data specification and software support tools.
description: The source of this description is the metadata record on FAIRsharing.org, an educational and informative resource that describes and links databases, standards, and data policies. FAIRsharing also creates collections of these resources and recommendations of databases and standards based on 3rd party data policies.
DOI: 10.25504/fairsharing.49bmk
title: FAIRsharing record for: AnaEE Thesaurus
title: anaeeThes

description: This FAIRsharing record describes:  The anaeeThes thesaurus aims at providing a controlled vocabulary for the semantic description of the study of continental ecosystems and their biodiversity. The thesaurus consists of concepts handled in different main thematic areas: abiotic (e.g. atmosphere, climate, hydrosphere, litosphere); biotic (e.g. animals, plants, micro-organisms, biodiversity); chemical compounds; experimentation and observation (e.g. instrument, method, protocol, measurement, quality, infrastructure); ecosystems (e.g. type, structure, functioning); modeling (e.g. formalism, platform, type of model, computer language); disciplines (disciplinary and scientific fields); and unit (units of the international system, inherited from the OBOE-standards ontology).
description: The source of this description is the metadata record on FAIRsharing.org, an educational and informative resource that describes and links databases, standards, and data policies. FAIRsharing also creates collections of these resources and recommendations of databases and standards based on 3rd party data policies.
DOI: 10.25504/fairsharing.7c8459
title: FAIRsharing record for: Visual Syntax Method
title: VSM

description: This FAIRsharing record describes:  VSM (Visual Syntax Method) is a set of principles for representing knowledge in a form that is easily understandable by both humans and machines – esp. by people without specialization in IT or Math.
| 
- The principles are universal, i.e. they support knowledge/thoughts/ideas on any topic, no matter the complexity.
- The principles are elementary and intuitive; they work 'like humans think'. This makes VSM scalable, and flexible on par with natural language.
- The principles describe how to Structure, Layout, and Interpret the meaning of a unit of knowledge 'in VSM form'; i.e. as a meaningful, precise, semi-linear structure that connects readable terms backed by semantic IDs.

VSM has a supporting user-interface called 'vsm-box', for reading and entering knowledge in VSM form.
 
| For an overview, see https://vsm.github.io
| For a video, see https://youtu.be/0kHWBZIL04E
| For conceptual details, see https://www.preprints.org/manuscript/202007.0486/v2
| For technical details, see https://github.com/vsm/vsm-box/blob/master/Documentation.md
description: The source of this description is the metadata record on FAIRsharing.org, an educational and informative resource that describes and links databases, standards, and data policies. FAIRsharing also creates collections of these resources and recommendations of databases and standards based on 3rd party data policies.
DOI: 10.25504/fairsharing.m2nu20
title: FAIRsharing record for: Citation File Format
title: CFF

description: This FAIRsharing record describes:  The Citation File Format (CFF) is a human-centric, machine-readable format for software citation metadata. It is developed to provide an easy way for RSEs, and other developers of software in academia, to ensure that they can receive credit for their work; likewise, it provides researchers with access to the necessary metadata for references to the software they use in their research. The Citation File Format follows the Software Citation Principles, and is compatible with the CodeMeta JSON-LD exchange format for software metadata.
description: The source of this description is the metadata record on FAIRsharing.org, an educational and informative resource that describes and links databases, standards, and data policies. FAIRsharing also creates collections of these resources and recommendations of databases and standards based on 3rd party data policies.
DOI: 10.25504/fairsharing.npmpqg
title: FAIRsharing record for: Biomedical Research Integrated Domain Group Model
title: BRIDG

description: This FAIRsharing record describes:  BRIDG is a domain analysis model that represents the realm of protocol-driven clinical, pre-clinical, translational and basic research. This breadth includes concepts from Common (i.e., concepts shared by all research protocols), Protocol Representation, Study Conduct, Adverse Events, Biospecimen, Molecular Biology, Experiment, Statistical Analysis and Regulatory subdomains. These research concepts provide a shared understanding of biomedical semantics (i.e., what each concept means and how it relates to other concepts) so that these semantics can be easily understood by subject matter experts in the biomedical domain.
description: The source of this description is the metadata record on FAIRsharing.org, an educational and informative resource that describes and links databases, standards, and data policies. FAIRsharing also creates collections of these resources and recommendations of databases and standards based on 3rd party data policies.
DOI: 10.25504/fairsharing.5970hq
title: FAIRsharing record for: OBOE: The Extensible Observation Ontology
title: OBOE

description: This FAIRsharing record describes:  OBOE is a suite of OWL-DL ontologies for modeling and representing scientific observations. The OBOE model is designed as a generic data model with a number of constructs for defining observational data. Key features of OBOE include its ability to represent a wide range of measurement types, a mechanism for specifying measurement context, and the ability to associate the type of entity (e.g., sample, organism, etc.) being measured. OBOE is being used and developed within the Semtools project for describing a wide variety of ecological data stored within the Knowledge Network for Biodiversity (KNB) as well as extensions for ontology-based data annotation and discovery within the MetaCat software infrastructure.
description: The source of this description is the metadata record on FAIRsharing.org, an educational and informative resource that describes and links databases, standards, and data policies. FAIRsharing also creates collections of these resources and recommendations of databases and standards based on 3rd party data policies.
DOI: 10.25504/fairsharing.9kahy4
title: FAIRsharing record for: GenBank Nucleotide Sequence Database
title: GenBank

description: This FAIRsharing record describes:  GenBank ® is the NIH genetic sequence database of annotated collections of all publicly available DNA sequences. GenBank is part of an International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Nucleotide Archive (ENA), and GenBank at NCBI. The GenBank database is designed to provide and encourage access within the scientific community to the most up-to-date and comprehensive DNA sequence information, and release available versioned collections every two months from the ftp site. As part of the International Nucleotide Sequence Database Collaboration (INSDC), a long-standing foundational initiative (operating between DDBJ, EMBL-EBI and NCBI), the INSDC covers the spectrum of data raw reads, through alignments and assemblies to functional annotation, enriched with contextual information relating to samples and experimental configurations. GenBank data submission types include:  mRNA sequences, Prokaryotic genes, Eukaryotic genes, rRNA and/or ITS, viral sequences, transposon or insertion sequences, microsatellite sequences, pseudogenes, cloning vectors, phylogenetic or population sets, and non-coding RNAs.

description: The source of this description is the metadata record on FAIRsharing.org, an educational and informative resource that describes and links databases, standards, and data policies. FAIRsharing also creates collections of these resources and recommendations of databases and standards based on 3rd party data policies.
DOI: 10.25504/fairsharing.m867wn
title: FAIRsharing record for: ADHDgene
title: ADHDgene

description: This FAIRsharing record describes:  A genetic database for attention deficit hyperactivity disorder. ADHDgene aims to provide research community with a central genetic resource and analysis platform for ADHD, to help unveil the genetic basis of ADHD and to contribute to global mental health.
description: The source of this description is the metadata record on FAIRsharing.org, an educational and informative resource that describes and links databases, standards, and data policies. FAIRsharing also creates collections of these resources and recommendations of databases and standards based on 3rd party data policies.
DOI: 10.25504/fairsharing.wvp1t7
title: FAIRsharing record for: GlycoNAVI
title: GlycoNAVI

description: This FAIRsharing record describes:  GlycoNAVI is a repository of data relevant to carbohydrate research. It contains a free suite of carbohydrate research tools organized by domain, including glycans, proteins, lipids, genes, diseases and samples.
description: The source of this description is the metadata record on FAIRsharing.org, an educational and informative resource that describes and links databases, standards, and data policies. FAIRsharing also creates collections of these resources and recommendations of databases and standards based on 3rd party data policies.
DOI: 10.25504/fairsharing.y2yct1
title: FAIRsharing record for: Allele frequency resource for research and teaching
title: ALFRED

description: This FAIRsharing record describes:  ALFRED is designed to make allele frequency data on human population samples readily available for use by the scientific and educational communities.
description: The source of this description is the metadata record on FAIRsharing.org, an educational and informative resource that describes and links databases, standards, and data policies. FAIRsharing also creates collections of these resources and recommendations of databases and standards based on 3rd party data policies.
DOI: 10.25504/fairsharing.e65js
title: FAIRsharing record for: Animal Transcription Factor Database
title: AnimalTFDB

description: This FAIRsharing record describes:  AnimalTFDB is a comprehensive animal transcription factor database. The resource is classification of transcription factors from 50 genomes from species including Homo sapiens and Caenorhabditis elegans. The database also has information on co-transcription factors and chromatin remodelling factors.
description: The source of this description is the metadata record on FAIRsharing.org, an educational and informative resource that describes and links databases, standards, and data policies. FAIRsharing also creates collections of these resources and recommendations of databases and standards based on 3rd party data policies.
DOI: 10.25504/fairsharing.s8vrb1
title: FAIRsharing record for: Apo and Holo structures DataBase
title: AH-DB

description: This FAIRsharing record describes:  AH-DB (Apo and Holo structures DataBase) collects the apo and holo structure pairs of proteins. Proteins are frequently associated with other molecules to perform their functions. Experimental structures determined in the bound state are named holo structures; while structures determined in the unbound state are named apo structures.
description: The source of this description is the metadata record on FAIRsharing.org, an educational and informative resource that describes and links databases, standards, and data policies. FAIRsharing also creates collections of these resources and recommendations of databases and standards based on 3rd party data policies.
DOI: 10.25504/fairsharing.9k7at4
title: FAIRsharing record for: Aspergillus Genome Database
title: ASPGD

description: This FAIRsharing record describes:  The Aspergillus Genome Database is a resource for genomic sequence data as well as gene and protein information for Aspergilli. This publicly available repository is a central point of access to genome, transcriptome and polymorphism data for the fungal research community.
description: The source of this description is the metadata record on FAIRsharing.org, an educational and informative resource that describes and links databases, standards, and data policies. FAIRsharing also creates collections of these resources and recommendations of databases and standards based on 3rd party data policies.
DOI: 10.25504/fairsharing.17r4y2
title: FAIRsharing record for: BuG@Sbase
title: BuG@Sbase

description: This FAIRsharing record describes:  BuG@Sbase is a microbial gene expression and comparative genomic database containing microarray datasets.
description: The source of this description is the metadata record on FAIRsharing.org, an educational and informative resource that describes and links databases, standards, and data policies. FAIRsharing also creates collections of these resources and recommendations of databases and standards based on 3rd party data policies.
DOI: 10.25504/fairsharing.ewjdq6
title: FAIRsharing record for: BioSamples
title: BioSD

description: This FAIRsharing record describes:  BioSamples, previously BioSample Database (BioSD), at the European Bioinformatics Institute stores and supplies descriptions and metadata about biological samples used in research and development by academia and industry. Samples are either 'reference' samples (e.g. from 1000 Genomes, HipSci, FAANG) or have been used in an assay database such as the European Nucleotide Archive (ENA) or ArrayExpress. It provides links to assays and specific samples, and accepts direct submissions of sample information.
description: The source of this description is the metadata record on FAIRsharing.org, an educational and informative resource that describes and links databases, standards, and data policies. FAIRsharing also creates collections of these resources and recommendations of databases and standards based on 3rd party data policies.
DOI: 10.25504/fairsharing.7x7ha7
title: FAIRsharing record for: Central Aspergillus Data REpository
title: CADRE

description: This FAIRsharing record describes:  This project aims to support the international Aspergillus research community by gathering all genomic information regarding this significant genus into one resource - The Central Aspergillus REsource (CADRE). CADRE facilitates visualisation and analyses of data using the Ensembl software suite. Much of our data has been extracted from Genbank and augmented with the consent of the original sequencing groups. This additional work has been carried out using both automated and manual efforts, with support from specific annotation projects and the general Aspergillus community.
description: The source of this description is the metadata record on FAIRsharing.org, an educational and informative resource that describes and links databases, standards, and data policies. FAIRsharing also creates collections of these resources and recommendations of databases and standards based on 3rd party data policies.
DOI: 10.25504/fairsharing.d8bfx4
title: FAIRsharing record for: Bitter Compounds Database
title: BitterDB

description: This FAIRsharing record describes:  BitterDB is a free and searchable database of bitter compounds. Compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste re- ceptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness.
description: The source of this description is the metadata record on FAIRsharing.org, an educational and informative resource that describes and links databases, standards, and data policies. FAIRsharing also creates collections of these resources and recommendations of databases and standards based on 3rd party data policies.
DOI: 10.25504/fairsharing.jr30xc
title: FAIRsharing record for: Bacterial protein tYrosine Kinase database
title: BYKdb

description: This FAIRsharing record describes:  The Bacterial protein tYrosine Kinase database (BYKdb) contains computer-annotated BY-kinase sequences. The database web interface allows static and dynamic queries and provides integrated analysis tools including sequence annotation.
description: The source of this description is the metadata record on FAIRsharing.org, an educational and informative resource that describes and links databases, standards, and data policies. FAIRsharing also creates collections of these resources and recommendations of databases and standards based on 3rd party data policies.
DOI: 10.25504/fairsharing.nj4vca
title: FAIRsharing record for: canSAR
title: null

description: This FAIRsharing record describes:  canSAR is an integrated cancer research and drug discovery resource that brings together large-scale data from different disciplines and allows query and exploration to help cancer research and drug discovery.
description: The source of this description is the metadata record on FAIRsharing.org, an educational and informative resource that describes and links databases, standards, and data policies. FAIRsharing also creates collections of these resources and recommendations of databases and standards based on 3rd party data policies.