FOODON - Foodon v2025-02-01

A new release with 0 ODK critical ERROR report items, compared with last weeks report! We still have thousands of missing food product definition and duplicate synonym term work to do, and looking forward to making big inroads on this in the coming month.

What's Changed

• Anoosha duplicated def by @Anoosha-Sehar in https://github.com/FoodOntology/foodon/pull/323

Full Changelog: https://github.com/FoodOntology/foodon/compare/2025-01-29...2025-02-01

Sustainable Development - Taxonomy and Ontology - Python
Published by ddooley 3 months ago

FOODON - FoodOn v2025-01-29

FoodOn has been upgraded to use the latest ODK build tool. This adds many more quality control queries as well as thousands of terms created via a new Animal term template. We still have a sizeable number of food product terms without definitions but that will be resolved within the next year.

Sustainable Development - Taxonomy and Ontology - Python
Published by ddooley 3 months ago

FOODON - FoodOn v2024-07-12

Many revisions and new terms including over 400 plant terms for PTFI project; a refreshed ONS dietary terms branch; some meal types; and an upper hierarchy of hazardous food terms.

Sustainable Development - Taxonomy and Ontology - Python
Published by ddooley 10 months ago

FOODON - FoodOn v2024-06-17

Many minor improvements:

• fixing errant owl:deprecated true values.
• animal parts update
• harmonizing hen X ... -> chicken X ...; shelled -> "shell on"
• merging "avian" and "avian animal"
• Removing LanguaL import annotation since hasDbXref to LanguaL indicates source, and more annotations are being added on.
• shucked -> shell off
  ...

Sustainable Development - Taxonomy and Ontology - Python
Published by ddooley 10 months ago

FOODON - FoodOn v2024-04-07

Adjustment to include in food product hierarchy a number of animal materials.
Eliminating duplicate labels.

Sustainable Development - Taxonomy and Ontology - Python
Published by ddooley about 1 year ago

FOODON - FoodOn v2024-03-26

Over 140 terms added to support PTFI (Periodic Table of Food Initiative) sample categories.

Sustainable Development - Taxonomy and Ontology - Python
Published by ddooley about 1 year ago

FOODON - FoodOn v2024-02-21

Introducing the Animal template, located in /src/ontology/imports/animal/, which generates the animal_parts.ofn import file based on an animal_parts.tsv file of anatomical parts x taxa, in conjunction with a species_list.tsv file that specifies all animals (common names and taxa) to generate parts for, and a further id_mapping_table.tsv which keeps track of existing FoodOn ids minted for this template. The id_integer.txt file indicates starting range of id's to mint for new terms.

Sustainable Development - Taxonomy and Ontology - Python
Published by ddooley about 1 year ago

FOODON - FoodOn v2024-02-03

This is an interim release, fixing a DL validation error. A release with animal parts template will come shortly.
This release also reduces the number of ChEBI annotations. Going forward for cross-references one can retrieve them directly from ChEBI.

Sustainable Development - Taxonomy and Ontology - Python
Published by ddooley about 1 year ago

FOODON - FoodOn v2023-12-18

This release contains many updates, including a new more comprehensive beef, pork, buffalo, and bison cuts section as well as preparation for a generic animal parts and plant parts templates to be launched soon.

Sustainable Development - Taxonomy and Ontology - Python
Published by ddooley over 1 year ago

FOODON - FoodOn v2023-06-30

This release contains numerous smaller edits, expansion of the plant taxa x anatomy robot table, adding namespace to various dbXrefs, and has been validated by Apache Jena riot validation tool to identify any errant RDF literals and URIs.

Sustainable Development - Taxonomy and Ontology - Python
Published by ddooley almost 2 years ago

FOODON - v0.5.1 release

• Deprecated some vitamin terms and replaced with CDNO hierarchy, CHEBI re-import.
• Removed use of NCIT Vitamin.
• Wine Biohackathon maceration terms, pomace, must, some preliminary appellation terms.
• Many curated FDA Seafood fish terms.

Sustainable Development - Taxonomy and Ontology - Python
Published by ddooley over 3 years ago

FOODON - v0.5 release

This release includes a refactor and addition of many organismal material food items - i.e. plant anatomical part x taxonomy - which are detailed in first tab of https://docs.google.com/spreadsheets/d/1VJtz4m67tdUNDqRe3m1Okdxll64nTR46GSvCOmb0APE

Sustainable Development - Taxonomy and Ontology - Python
Published by ddooley almost 4 years ago

FOODON - FoodOn Beta v0.4.8 release

This release brings the replacement of over 1,600 foodon plant and animal species terms with their NCBITaxon equivalents, which now carry all the annotations that the foodon terms had. The separation previously existed because NCBITaxon entities were not thought to necessarily be references to whole organisms, but this attitude is now clear, thus removing the need for corresponding FoodOn entities. A next task will be to ensure as many remaining foodon plant and animal entities can be associated with NCBITaxon as possible; however NCBITaxon isn't a comprehensive taxonomy as it covers only sequenced organisms.

Sustainable Development - Taxonomy and Ontology - Python
Published by ddooley over 4 years ago

FOODON - FoodOn Alpha v0.4.7 release

Numerous updates, including removal of a bad equivalence on "mammal" class.

Sustainable Development - Taxonomy and Ontology - Python
Published by ddooley almost 5 years ago

FOODON - FoodOn Alpha v0.4.6 release

Many term edits to support text-mining; as well beginning nutritional measurement datum term support. Switched to RO 'in taxon' from 'has taxonomic identifier'

Sustainable Development - Taxonomy and Ontology - Python
Published by ddooley about 5 years ago

FOODON - FoodOn Alpha v0.4.5 release

Includes edits for upcoming FOBI ontology for food biomarkers.

Sustainable Development - Taxonomy and Ontology - Python
Published by ddooley over 5 years ago

FOODON - FoodOn Alpha v0.4.4 release

Involves numerous edits to food products that required entries or synonyms in ordere to match to LexMapr biosample datasets.

Sustainable Development - Taxonomy and Ontology - Python
Published by ddooley over 5 years ago

FOODON - FoodOn Alpha v0.4.3 release

Numerous edits including shortened food source labels, and 30+ SciBite requests.

Sustainable Development - Taxonomy and Ontology - Python
Published by ddooley about 6 years ago

FOODON - FoodOn Alpha v0.4.2 release

Correction - previous release was supposed to have Nov 1 content, which this one now has.

Sustainable Development - Taxonomy and Ontology - Python
Published by ddooley over 6 years ago

FOODON - FoodOn Alpha v0.4.1 release

Numerous term edits; simplified ENVO import; 460 terms remaining in "to be processed" list.

Sustainable Development - Taxonomy and Ontology - Python
Published by ddooley over 6 years ago

FOODON - FoodOn Alpha v0.4.0 release

The major work done in this version is the inclusion of over 9,000 food product categories derived from the LanguaL indexed SIREN database (http://www.langual.org/langual_indexed_datasets.asp) directly into foodon.owl. Previously they were in a very tentative hierarchy in the subset_siren_import.owl file. These are now positioned under a "food product type" -> "foodon product type" tree (along with food products inherited from ENVO). This is the native FoodOn product hierarchy; other agency and miscellaneous categorizations are also apparent under "food product type". An effort in the next year will be to cross reference FoodOn's native categories with the others. We will also be adding Wikipedia definitions where the connection is obvious. Note that an outstanding list of over 600 "food product type (to be processed)" items remain to be categorized but is included in that class for identifier retrieval in the meantime.

Sustainable Development - Taxonomy and Ontology - Python
Published by Public-Health-Bioinformatics almost 7 years ago

FOODON - FoodOn Alpha v0.3.1 release

This release adjusts one aspect of FoodOn that was a bit odd, namely that this brand new ontology came with hundreds of deprecated terms. These items haven't been in circulation as FoodOn terms. These terms exist only to facilitate import of existing LanguaL food indexed database items, in order to keep track of food items that need their logical equivalency axiom to be revised. FoodOn deprecated all of LanguaL's "[food item] added" terms, and replaced many with references to "has substance added" some "[food item]". This update sequesters all deprecated terms to a langual_deprecated_import.owl file, and revises the subset_siren_import.owl to reference deprecated terms appropriately.

Sustainable Development - Taxonomy and Ontology - Python
Published by Public-Health-Bioinformatics about 8 years ago

FOODON - FoodOn Alpha v0.2 release

This release incorporates the major work done to import all the LanguaL.org food indexing system facets as well as cross-reference of food source items to NCBI taxonomy, the inclusion of cultural (ancestro ontology) origin terms. It also includes a large database of over 9000 food terms from the SIREN food database. This is linked from the foodon.owl file; for a more core version that does not include these terms, use the foodon_core.owl file.

Sustainable Development - Taxonomy and Ontology - Python
Published by Public-Health-Bioinformatics about 8 years ago

FOODON - 2016-03-21

This is a test release, trialling the ontology starter kit workflows. The release files in src/ should be empty.

Sustainable Development - Taxonomy and Ontology - Python
Published by pbuttigieg about 9 years ago