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Semantic Mapping Resources

  1. iSamples
  2. Darwin Core
  3. SSSOM Mapping Specification
  4. Semantic Mapping Vocabulary
  5. LinkML

iSamples

Resources

Title URL Description
iSamples GitHub Home https://isamplesorg.github.io/home/ Project landing page on GitHub
Zenodo Community https://zenodo.org/communities/isamples/records Landing page of the iSamples Community on Zenodo
iSamples GitHub Organization Home https://github.com/isamplesorg Organization landing page for iSamples
iSamples Metadata Repository https://github.com/isamplesorg/metadata Metadata repository for iSamples
iSamples Metadata Documentation https://isamplesorg.github.io/metadata/ Documentation that describes the metadata in the metadata repository
LinkML Registry Profile https://linkml.io/linkml-registry/registry/#isamples LinkML is a flexible modeling language that allows you to author schemas in YAML that describe the structure of your data.
iSamples GitHub Site https://isamplesorg.github.io/ The landing page for the GitHub pages iSamples site
Overview of iSamples Sample Description Scheme https://zenodo.org/records/7434185 Presentation that provides an overview of iSamples published as a pdf on Zenodo
iSamples API Documentation https://hyde.cyverse.org/isamples_central/docs Swagger Docs that describe the iSamples Portal API
iSamples Search Portal https://hyde.cyverse.org/isamples_central/ui/#/ Frontend interface for searching iSamples data

Publications

  • Davies N, Deck J, Kansa EC, Kansa SW, Kunze J, Meyer C, Orrell T, Ramdeen S, Snyder R, Vieglais D, Walls RL, Lehnert K (2021). Internet of samples (iSamples): Toward an interdisciplinary cyberinfrastructure for material samples. GigaScience, 10(5), giab028.
  • Song H, Cui H, Vieglais D, Mandel D, Thomer AK (2023) Automated Metadata Enhancement for Physical Sample Record Aggregation in the iSamples Project. Proceedings of the Association for Information Science and Technology, 60(1), 1131-1133.
  • Richard SM, Vieglais D, Thomer A, Song H, Davies N, Deck J, Gan Q, Kansa EC, Kansa S, Kunze J, Lehnert K (2024) A metadata schema for documenting material samples from multiple domains. Semantic Web In press.

Darwin Core

Resources

Title URL Description
Darwin Core Home https://dwc.tdwg.org/ The TDWG website homepage of Darwin Core
Simple Darwin Core https://dwc.tdwg.org/simple/ A simplified version of the normative documentation for general usage of the standard
Quick Reference Guide https://dwc.tdwg.org/terms/ The summarized normative documentation
Normative Documentation https://dwc.tdwg.org/list/ The official, normative, TDWG-compliant documentation of the Darwin Core standard
Simple Horizontal Template https://github.com/tdwg/dwc/blob/master/dist/simple_dwc_horizontal.csv A blank template with terms as column headers
Simple Vertical Template https://github.com/tdwg/dwc/blob/master/dist/simple_dwc_vertical.csv A blank template with a single column containing all terms in Simple Darwin Core
Vertical Template https://github.com/tdwg/dwc/blob/master/dist/all_dwc_vertical.csv A blank template with a single column containing the complete set of Darwin Core terms
Main GitHub Repository https://github.com/tdwg/dwc Primary repository of the Darwin Core standard
Questions and Answers Forum https://github.com/tdwg/dwc-qa/blob/master/README.md A GitHub repo dedicated to questions and answers about the Darwin Core standard.

SSSOM

Title URL Description
Simple Standard for Sharing Ontological Mappings (SSSOM) https://mapping-commons.github.io/sssom/ The Simple Standard for Sharing Ontological Mappings (SSSOM) is a community-driven standard designed to facilitate the exchange and integration of semantic entity mappings.
SSSOM Official Data Model Documentation https://mapping-commons.github.io/sssom/linkml-index/ Datamodel for Simple Standard for Sharing Ontological Mappings (SSSOM)

Semantic Mapping Vocabulary

Title URL Description
Semantic Mapping Vocabulary Documentation https://mapping-commons.github.io/semantic-mapping-vocabulary/ A matching process that exploits background knowledge from external resources, commonly referred to as background knowledge resources. This approach is also known as indirect matching, BK-based matching or context-based matching.
Semantic Mapping Vocabulary GitHub Repo https://github.com/mapping-commons/semantic-mapping-vocabulary The Semantic Mapping Vocabulary (SEMAPV) is a vocabulary about the processes, entities and agents involved in the curation of mappings.

LinkML

Title URL Description
LinkML Metamodel https://linkml.io/linkml-model/latest/docs/home/ This specification provides a grammar for a functional syntax for expressing the structure of LinkML instances. A LinkML instance is a tree-like structure conforming to the syntax specified here.
Landing Page https://linkml.io/linkml/ LinkML is a flexible modeling language that allows you to author schemas in YAML that describe the structure of your data. Additionally, it is a framework for working with and validating data in a variety of formats (JSON, RDF, TSV), with generators for compiling LinkML schemas to other frameworks.