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TermMapping
Ellmer type schema for a single ontology term mapping
TermMappingTable
Ellmer type schema for a table of ontology term mappings
allmap
map from biocViews to EDAM
bioc_line()
use BiocPkgTools to acquire metadata on a specified Bioconductor package
biotools_bioc
result of scanning biotools metadata on 3 Nov 2024 to find bioconductor packages and EDAM topics
bvbrowse()
interactive exploration of biocViews in relation to packages
cleantxt()
utility to "clean" odd characters in text input that seem to increase risk of LLM failures
curate_bioc()
use Anh Vu's prompting to develop structured metadata about Bioconductor packages, targeting EDAM ontology and bio.tools schema
edam_data
snapshot of edam data circa early 2024
edam_formats
snapshot of edam formats circa early 2024
edam_graph()
build a graph of EDAM terms deemed relevant to a text
edam_operations
snapshot of edam operations circa early 2024
edam_topics
snapshot of edam topics circa early 2024
edamize()
Assign EDAM ontology terms to text using a live SemanticSQL database and an LLM
extract_uri()
Helper recursive function to extract 'uri' nodes from JSON document based on edamize
flat_tagger()
simple tagger based on text excerpt and available context from data-frames with edam vocabularies
get_edam_embeddings()
Retrieve pre-computed EDAM term embeddings from AnnotationHub
llm_api_key()
Retrieve the API key for an LLM provider from the environment
llm_chat()
Create an ellmer chat object for a given LLM provider
llm_env_var()
Map an LLM provider name to its environment variable
make_edam_embeddings()
Generate and save EDAM term embeddings
map_concepts()
Map biological or medical concepts to ontology terms via OLS4
map_concepts_edam()
Map concepts to EDAM ontology terms via OLS4
mapping_to_json()
Export a map_concepts result as a JSON document
mkdf()
simple utility to process output of edamize into a data.frame
ols4_chat()
Create an ellmer chat pre-wired with EBI OLS4 MCP tools
ols4_enrich()
Validate and enrich a TermMappingTable via the OLS4 REST API
ols4_mcp_tools()
List tools available from the EBI OLS4 MCP service
ols4_tool_table()
Summarise OLS4 MCP tools as a data frame
pksByViews()
helper for package listing
read_prompt()
Read a prompt template from the biocEDAM prompt library
retrieve_edam_candidates()
Retrieve the top-k semantically closest EDAM terms per type
saved_views_2023.18.11
dated set of biocViews
tag_bioc()
full workflow to tag a bioconductor package and selected representative content with EDAM terms
toline()
process the output of edamize followed by mkdf to create a data frame with components topic, operation, data, format, reflecting main elements of EDAM
verify()
given a data.frame with uri and tm produced by edamize (or mkdf), check against the frozen EDAM term tables in biocEDAM, filtering records to those whose uri matches a known id.
vig2data()
Use the extract_data facility defined in ellmer's doc to obtain summary information about textual content. Originally tailored to vignettes in bioconductor; it is newly generalized to handle any pdf, html or text in URL.
vlist
snapshot of all biocViews