food-microbiome-habitats

Format bacteria habitat predictions for the FoodMicrobiome project

Sources (not included in the repo):

• PubMed abstracts
• GenBank
• DSMZ
• CIRM

Named entity recognition (taxon names and habitat mentions), normalization (habitats) and relation extraction (lives in): openminted/UC-AS-C.

make -n output/food-microbiome-habitats

prepare-food-microbiome.py : main script for building the table. It requires the following resources:

resources/taxa+id_Bacteria.txt : synonym map of bacteria taxa.

predictions/PubMed_lives-in.txt, predictions/genbank_mappings.txt, predictions/dsmz-taxon-habitat-mappings.txt, predictions/CIRM_08022018.txt : taxon-habitat predictions.

etc/habitat-focus.txt : identifier and label for habitat focus concepts.

Explore and prepare BioSample input

File dimension reduction

Goal: filter bacteria samples and split into several files.

make -n resources/biosample-split

resources/biosample_set.xml : complete BioSample as downloaded from NCBI.

Explore the usage of Attributes

Goal: inventory of all Attributes used in BioSample entries.

make -n output/biosample-attributes-count.txt

Explore candidate Attributes for habitats

Goal: evaluate the amount of habitat information found in BioSample.

make -n output/biosample-table.txt