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Data from: Tripal EUtils - A Tripal module to increase exchange and reuse of genome assembly metadata

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posted on 2024-02-15, 20:18 authored by Bradford Condon, Abdullah Almsaeed, Sean Buehler, Christopher Childers, Stephen Ficklin, Margaret Staton, Monica PoelchauMonica Poelchau

A core component of NCBI’s BioSample metadata are the BioSample “packages” (https://www.ncbi.nlm.nih.gov/biosample/docs/packages/). Data submitters can choose a package, which contain a variety of attribute sets, such as plant- or insect-specific attributes, attribute values as recommended by the MIxS standard, etc. Here, we provide suggested ontology term mappings for attributes from the Invertebrate 1.0 and Plant 1.0 packages (https://www.ncbi.nlm.nih.gov/biosample/docs/packages/Invertebrate.1.0/, https://www.ncbi.nlm.nih.gov/biosample/docs/packages/Plant.1.0/). This dataset corresponds to Table 4 in the corresponding publication in the journal Database.


Resources in this dataset:

  • Resource Title: Ontology term mapping from: Tripal EUtils - A Tripal module to increase exchange and reuse of genome assembly metadata.

    File Name: Table4-ontology-mappings.csv

    Resource Description: Proposed property mappings from the NCBI BioSample attribute packages for invertebrates and plants to ontology terms. Where no ontology terms were found, fields are left blank.


  • Resource Title: Data dictionary for Ontology term mapping.

    File Name: data_dictionary.csv

Funding

USDA-ARS

National Science Foundation: 1444573

History

Data contact name

Poelchau, Monica

Data contact email

monica.poelchau@usda.gov

Publisher

Ag Data Commons

Intended use

The ontology term mappings are intended to be used by other databases that provide NCBI BioSample metadata from the Invertebrate 1.0 (https://www.ncbi.nlm.nih.gov/biosample/docs/packages/Invertebrate.1.0/) and Plant 1.0 (https://www.ncbi.nlm.nih.gov/biosample/docs/packages/Plant.1.0/) packages

Use limitations

These mappings should be deprecated if NCBI publishes their own ontology term mappings for these packages.

Theme

  • Not specified

ISO Topic Category

  • biota

Ag Data Commons Group

  • Insects - i5K

National Agricultural Library Thesaurus terms

genome assembly; invertebrates

OMB Bureau Code

  • 005:00 - Department of Agriculture

Pending citation

  • No

Public Access Level

  • Public

Preferred dataset citation

Condon, Bradford; Almsaeed, Abdullah; Buehler, Sean; Childers, Christopher; Ficklin, Stephen; Staton, Margaret; Poelchau, Monica (2019). Data from: Tripal EUtils - A Tripal module to increase exchange and reuse of genome assembly metadata. Ag Data Commons. https://doi.org/10.15482/USDA.ADC/1505452

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