Hello, I would like to understand how to use an ENVO ontology obo file (https://github.com/EnvironmentOntology/envo) for annotating plain text. I'm encountering difficulty finding a program or library capable of annotating plain text with ontology tags. Most search results seem to focus on creating ontologies, whereas I already possess one. I'm unsure if a tool for this purpose exists, but I'm curious about the practical application of an ontological dictionary if not for this.
Here's an example (fusion from various columns of informations):
Sequel sequencing of SAMD00319324 KatS3 sediment Sequel sequencing of SAMD00319324" | The objective of this study is to ascertain the metabolic potentials of microbial communities in Japanese hot springs. | Hot spring metagenomics | Metagenomics of Katase hot spring sample | freshwater biome | Japan: Shizuoka: Higashi-izu: Arayu | thermophilic sediment | neutral hot spring
I would like to achieve the following annotations:
ENVO_00000051 (hot spring)
ENVO_00000873 (freshwater biome)
ENVO_01000132 (thermophilic sediment)
ENVO_01001897 (neutral spring)
Additionally, I wish for the annotation to be robust, accounting for misspelled text as well. Furthermore, I'd like to supplement this ontology with additional terms. In the ENVO dictionary, only "cryoconite deposit" and "cryoconite hole" are available, so I don't think it will match when I have this kind of text:
Investigating the Biotechnological Potential of Arctic Bacteria | Cryoconite | ...
I have experimented with the python libraries nltk, re, difflib but I'm only searching for the label's name in the obo file to see if it matches with the text.
Thank you in advance for your assistance.
