Difference between revisions of "Links"
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[https://isa-specs.readthedocs.io/en/latest/ '''ISA Model and Serialization Specifications'''] with [https://isa-specs.readthedocs.io/en/latest/isamodel.html ISA Abstract Model] (three core entities to capture experimental metadata: investigation, study, assay) and ISA tools under https://isa-specs.readthedocs.io/en/latest/implementations.html and https://github.com/ISA-tools | [https://isa-specs.readthedocs.io/en/latest/ '''ISA Model and Serialization Specifications'''] with [https://isa-specs.readthedocs.io/en/latest/isamodel.html ISA Abstract Model] (three core entities to capture experimental metadata: investigation, study, assay) and ISA tools under https://isa-specs.readthedocs.io/en/latest/implementations.html and https://github.com/ISA-tools | ||
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| + | '''[http://www.researchobject.org/ RO- Crate Initiative]''': RO-Crate has been developed as a schema.org-based JSON lightweight approach to the next generation '''Research Object serialization'''. | ||
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'''GFBio Overview on "Concepts and Standards":''' [http://gfbio.biowikifarm.net/wiki/Data_exchange_standards,_protocols_and_formats_relevant_for_the_collection_data_domain_within_the_GFBio_network Data exchange standards, protocols and formats relevant for the collection data domain] | '''GFBio Overview on "Concepts and Standards":''' [http://gfbio.biowikifarm.net/wiki/Data_exchange_standards,_protocols_and_formats_relevant_for_the_collection_data_domain_within_the_GFBio_network Data exchange standards, protocols and formats relevant for the collection data domain] | ||
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| + | [https://www.ogc.org/standards/sensorml '''SensorML Standard'''], see also [https://en.wikipedia.org/wiki/SensorML Wikipedia Site SensorML] | ||
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| + | [https://github.com/rdawg-pidinst/schema '''Metadata Schema for the Persistent Identification of Scientific Instruments'''], see [https://www.rd-alliance.org/groups/persistent-identification-instruments-wg PIDINST RDA WG] and [https://arxiv.org/abs/2003.12958 Stocker et al. 2020] | ||
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DONA Foundation. (2019). Digital Object Architecture. Available at: https://www.dona.net/digitalobjectarchitecture . with "digital object concept" | DONA Foundation. (2019). Digital Object Architecture. Available at: https://www.dona.net/digitalobjectarchitecture . with "digital object concept" | ||
| − | [https://rd-alliance.github.io/metadata-directory/standards/ | + | [https://rd-alliance.github.io/metadata-directory/standards/ RDA Metadata Standards Directory] |
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| + | odMLtables: A User-Friendly Approach for Managing Metadata of Neurophysiological Experiments, see [https://www.frontiersin.org/articles/10.3389/fninf.2019.00062/full article] | ||
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| + | geodomain-specific ISO Norms [https://de.wikipedia.org/wiki/ISO_19115 ISO 19115], see also https://www.forschungsdaten.org/index.php/ISO_19115) | ||
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| + | [http://bioguid.org/about BioGUID Registry] - service for indexing and cross-linking identifiers for data objects within the realm of Biodiversity informatics (outdated?) | ||
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| + | RuleML HITS Heidelberg | ||
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| + | SEEK, Rightfield | ||
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| + | FAIRDO.org | ||
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Latest revision as of 17:00, 6 July 2021
Consortia for standards recommendations
Genomic Standards Consortium (GSC) with GBWG working group
Biodiversity Information Standards (TDWG)
Concepts, schemes and exchange standards, metastandards (* mapped with MOD-CO schema)
MIxS Scheme with Terms in TDWG Wiki with five vocabularies included, e. g. MIxS Environment Vocabulary * (primary representation; LOD compliant)
GSC MIxS: The GSC family of minimum information standards (checklists) – Minimum Information about any (x) Sequence; MIxS currently consists of three separate checklists; MIGS for genomes, MIMS for metagenomes, and MIMARKS for marker genes. The three checklists that are currently under MIxS share the same central set of core descriptors, but have checklist specific descriptors as well. Additionally, they enable a detailed description of environment through the use of 15 optional environmental packages.
see also MIxS – Minimum information about any (x) sequence ENA Checklist
ABCD 2 Data Standard, ratified version * and ABCD 2 Data Standard (LOD-compliant representation)
ABCD 3 with ABCD 3.0 xml schema documentation
GGBN Data Standard v. 1 and GGBN Data Standard * (LOD-compliant representation); with e. g. relation to DwC http://wiki.ggbn.org/ggbn/DwC; see also Global Genome Biodiversity Network (GGBN) Portal and GGBN Wiki
Darwin Core with Darwin Core Terms: A quick reference guide * (primary representation) and Darwin Core (experimental LOD-compliant representation, attention, might not be actual)
SDD Standard Description Download and SDD Schema files SDD1.1rev5
TDWG Terms Wiki: Help with definitions of scheme, standard and term and 29 concept schemes included
ISA Model and Serialization Specifications with ISA Abstract Model (three core entities to capture experimental metadata: investigation, study, assay) and ISA tools under https://isa-specs.readthedocs.io/en/latest/implementations.html and https://github.com/ISA-tools
RO- Crate Initiative: RO-Crate has been developed as a schema.org-based JSON lightweight approach to the next generation Research Object serialization.
Minimum Information About a Plant Phenotyping Experiment - MIAPPE with https://github.com/MIAPPE
AnIML Markup Language. The Analytical Information Markup Language (AnIML) is the emerging ASTM XML standard for analytical chemistry and biological data; see Core schema and paper https://www.laboratory-journal.com/category/tags/data-exchange and paper: https://journals.sagepub.com/doi/10.1016/j.jala.2004.10.003; BSSN software GmbH
Consortium for Standardization in Lab Automation (SiLA) develops and introduces new device and data interface standards with SiLA 2 Core and Mapping specification https://docs.google.com/document/d/1-shgqdYW4sgYIb5vWZ8xTwCUO_bqE13oBEX8rYY_SJA/edit , IPA Fraunhofer Stuttgart: Labor-IT and SiLA
ASTM Subcommittee on analytical data E13.15, E1578 standard for laboratory informatics
Federal Geographic Data Committee Biological Data Working Group and U.S. Geological Survey Biological Resources Division [FGDC].1999. Content standard for digital geospatial metadata - biological data profile, FGDC-STD-001.1-1999. Federal Geographic Data Committee, Washington, D.C., USA., see https://www.fgdc.gov/metadata/csdgm-standard - CSDGM-Biological Data Profile (BDP)
GBIF Resources: This site contains technical GBIF resources like XML schemas, Darwin Core Archive/IPT extensions and vocabularies and is primarily intended for machine reading; see xml schema EML 2.1.1, GGBN extension of DwC etc.
GFBio Overview on "Concepts and Standards": Data exchange standards, protocols and formats relevant for the collection data domain
SensorML Standard, see also Wikipedia Site SensorML
Metadata Schema for the Persistent Identification of Scientific Instruments, see PIDINST RDA WG and Stocker et al. 2020
Knowledge Organisation Systems, Ontology Vocabularies
SKOS Simple Knowledge Organization System
http://terms.tdwg.org/wiki/Simple_Knowledge_Organization_System
Biological Collections Ontology (BCO) based on Basic Formal Ontology and DwC terms
SPREC schema with draft International Standard, ISO/DIS 20387 for biobanking
DWB namespaces and ER diagrams
DiversityCollection information models *
DiversityDescriptions information models
Databases for implementation of MOD-CO ontologies/ vocabularies and schemas
Links of Interest
Ontology Metadata Vocabulary - OMV, Description
EDAM Ontology: An ontology of biological and biomedical topics, created from merging the EDAM Topics sub-ontology with auxiliary topics that are out of scope of EDAM, used by bio.tools
LIMS Laboratory information management system, see list of software, e.g. LabCollector with Installation Wizard etc. see LIMS Get started; company AgileBio; online demo
ELN Electronic laboratory notebook, in R&D labs, see list of software, e.g. LabCollector
ELN versus LIMS "Ein LIMS ist darauf ausgelegt, Daten hoch strukturiert abzulegen, ein ELN (electronic laboratory notebook) ist darauf ausgelegt, Daten unstrukturiert abzulegen." Protokolle in ELN, ELN in F&E Laboren...
Build LIMS yourself or buy a commercial LIMS?. The Company softwarepoint is the LabVantage company in the Northern Europe, founded in Finland.
Biobanking LIMS, Company softwarepoint
Marktübersicht LIMS mit LIMS Grundlagen ... https://www.lims.de/index.html
BIOAWARE company: Life Sciences Data Management Software, Limsophy LIMS and RIMS, bei IPK Gatersleben
ISO 25964 – the international standard for thesauri and interoperability with other vocabularies
ISO/IEC 17025:2017 – General requirements for the competence of testing and calibration laboratories
Biowikifarm Software Documentation
Schema.org and Schema.org Vocabulary
Identifiers.org registry with data collections with own namespaces
zu "Online Registries: The DNS and Beyond... Handle DOI" Dyson 2003
Berners-Lee, T. (2006/2009): Linked Data. https://www.w3.org/DesignIssues/LinkedData.html
PROV standards: https://www.w3.org/TR/2013/NOTE-prov-overview-20130430/ and https://www.w3.org/2011/prov/wiki/Main_Page (incl. mapping to Dublin Core)
Fairsharing.org - A curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies, e.g., https://fairsharing.org/standards/?q=SDD : distinguish between Terminology Artifact; Model/Format and Reporting Guideline; 1118 standards, 262 of these models/formats, 160 of these life science, 11 biodiversity, 18 sequence
The Unicode Standard and Unicode Symbols
Sensordaten in der Cloud mit io-Key
Virtual informatics with laboratory informatics, bioinformatics, geoinformatics and biodiversity informatics
DONA Foundation. (2019). Digital Object Architecture. Available at: https://www.dona.net/digitalobjectarchitecture . with "digital object concept"
RDA Metadata Standards Directory
odMLtables: A User-Friendly Approach for Managing Metadata of Neurophysiological Experiments, see article
geodomain-specific ISO Norms ISO 19115, see also https://www.forschungsdaten.org/index.php/ISO_19115)
BioGUID Registry - service for indexing and cross-linking identifiers for data objects within the realm of Biodiversity informatics (outdated?)
RuleML HITS Heidelberg
SEEK, Rightfield
FAIRDO.org
TESTE:
8139d48b-f83f-49cc-81c6-b037f0bc8e6c
b01c8598-0aa0-45eb-a2cc-f67b54098191
http://mod-co.net/8139d48b-f83f-49cc-81c6-b037f0bc8e6c ??? wie UUID as html page head element “title“
