posted on 2024-02-15, 20:18authored byBradford Condon, Abdullah Almsaeed, Sean Buehler, Christopher Childers, Stephen Ficklin, Margaret Staton, Monica PoelchauMonica Poelchau
<p>A core component of NCBI’s BioSample metadata are the BioSample “packages” (<a href="https://www.ncbi.nlm.nih.gov/biosample/docs/packages/">https://www.ncbi.nlm.nih.gov/biosample/docs/packages/</a>). 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 (<a href="https://www.ncbi.nlm.nih.gov/biosample/docs/packages/Invertebrate.1.0/">https://www.ncbi.nlm.nih.gov/biosample/docs/packages/Invertebrate.1.0/</a>, <a href="https://www.ncbi.nlm.nih.gov/biosample/docs/packages/Plant.1.0/">https://www.ncbi.nlm.nih.gov/biosample/docs/packages/Plant.1.0/</a>). This dataset corresponds to Table 4 in the corresponding publication in the journal <em>Database</em>. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Ontology term mapping from: Tripal EUtils - A Tripal module to increase exchange and reuse of genome assembly metadata.</p> <p>File Name: Table4-ontology-mappings.csv</p><p>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. </p></li><br><li><p>Resource Title: Data dictionary for Ontology term mapping.</p> <p>File Name: data_dictionary.csv</p></li></ul><p></p>
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