Package: ducksemantics 0.2.1

Sounkou Mahamane Toure

ducksemantics: DuckDB-Native Semantic and Retrieval Relations

DuckDB-native ontology graphs, validated Human Phenotype Ontology (HPO) observations, typed release-cataloged Monarch relations including read-only projections of attached dated packs, provider/snapshot-catalog-bound literature retrieval, and source-grounded semantic judgments. Bulk values are ordinary relations; optional S7 protocols are reserved for real prompt, embedding, parser, and annotator providers. The package does not store ClinVar or PubMed source data, download Monarch packs, rank cases, or evaluate benchmarks.

Authors:Sounkou Mahamane Toure [aut, cre], Human Phenotype Ontology [cph]

ducksemantics_0.2.1.tar.gz
ducksemantics_0.2.1.zip(r-4.7-any)ducksemantics_0.2.1.zip(r-4.6-any)ducksemantics_0.2.1.zip(r-4.5-any)
ducksemantics_0.2.1.tgz(r-4.6-any)ducksemantics_0.2.1.tgz(r-4.5-any)
ducksemantics_0.2.1.tar.gz(r-4.7-any)ducksemantics_0.2.1.tar.gz(r-4.6-any)
ducksemantics_0.2.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ducksemantics/json (API)

# Install 'ducksemantics' in R:
install.packages('ducksemantics', repos = c('https://rgenomicsetl.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rgenomicsetl/ducksemantics/issues

Pkgdown/docs site:https://rgenomicsetl.github.io

On CRAN:

Conda:

2.88 score 3 stars 3 scripts 53 exports 4 dependencies

Last updated from:6d5f799ab0. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK89
source / vignettesOK203
linux-releaseOK94
macos-releaseOK69
macos-oldrelOK93
windows-develOK68
windows-releaseOK66
windows-oldrelOK62
wasm-releaseOK93

Exports:ducksemantics_annotateducksemantics_bebel_runnerducksemantics_bebel_tool_judgment_parserducksemantics_closure_sqlducksemantics_colbert_providerducksemantics_connectducksemantics_default_judgment_instructionsducksemantics_embedducksemantics_embedding_batchducksemantics_embedding_providerducksemantics_embedding_searchducksemantics_embeddinggemma_providerducksemantics_groundducksemantics_hpo_observation_contractducksemantics_hpo_observationsducksemantics_index_aliasesducksemantics_initducksemantics_json_judgment_parserducksemantics_judgeducksemantics_judgment_promptducksemantics_late_interaction_searchducksemantics_lexical_annotatorducksemantics_literature_retrieveducksemantics_literature_snapshot_catalogducksemantics_materialize_embedding_indexducksemantics_monarch_gene_disease_holdout_auditducksemantics_monarch_importducksemantics_monarch_project_packducksemantics_monarch_queryducksemantics_monarch_release_catalogducksemantics_normalizeducksemantics_parseducksemantics_projection_sqlducksemantics_prompt_runnerducksemantics_read_oboducksemantics_record_judgmentsducksemantics_runducksemantics_schema_sqlducksemantics_tablesducksemantics_token_embedducksemantics_token_embedding_batchducksemantics_token_embedding_batch_from_providerducksemantics_token_embedding_providerducksemantics_tokensducksemantics_write_embeddingsducksemantics_write_graphducksemantics_write_oboducksemantics_write_token_embeddingsDucksemanticsAnnotatorDucksemanticsEmbeddingProviderDucksemanticsJudgmentParserDucksemanticsPromptRunnerDucksemanticsTokenEmbeddingProvider

Dependencies:DBIglueS7s7contract

Readme and manuals

Help Manual

Help pageTopics
Generate lexical HPO/ontology candidatesducksemantics_annotate
Create a BebeLM prompt providerducksemantics_bebel_runner
Create a BebeLM tool-call judgment parserducksemantics_bebel_tool_judgment_parser
Materialize transitive closure SQLducksemantics_closure_sql
Create a native ColBERT providerducksemantics_colbert_provider
Connect to a DuckDB semantic storeducksemantics_connect
Default source-grounded judgment instructionsducksemantics_default_judgment_instructions
Construct embedding rowsducksemantics_embedding_batch
Wrap an embedding function as an embedding providerducksemantics_embedding_provider
Search dense embeddingsducksemantics_embedding_search
Create an EmbeddingGemma providerducksemantics_embeddinggemma_provider
HPO observation contractducksemantics_hpo_observation_contract
Validate accepted HPO observations against source documentsducksemantics_hpo_observations
Build the lexical alias indexducksemantics_index_aliases
Initialize semantic graph tablesducksemantics_init
Create a JSON judgment parserducksemantics_json_judgment_parser
Judge lexical candidates with a providerducksemantics_judge
Build a source-grounded judgment promptducksemantics_judgment_prompt
Exact token-level late-interaction searchducksemantics_late_interaction_search
Create the default lexical grounding providerducksemantics_lexical_annotator
Retrieve exact literature spans from append-only caller-owned relationsducksemantics_literature_retrieve
Validate an append-only literature snapshot catalogducksemantics_literature_snapshot_catalog
Materialize a fixed-dimension embedding tableducksemantics_materialize_embedding_index
Audit a historical Monarch gene-disease holdoutducksemantics_monarch_gene_disease_holdout_audit
Import caller-supplied Monarch relationsducksemantics_monarch_import
Project one attached, dated Monarch annotation packducksemantics_monarch_project_pack
Select one cataloged Monarch releaseducksemantics_monarch_query
Validate a typed Monarch release catalogducksemantics_monarch_release_catalog
Normalize semantic textducksemantics_normalize
Project edge-shaped data to graph SQLducksemantics_projection_sql
Wrap a prompt function as a prompt providerducksemantics_prompt_runner
Provider protocol genericsducksemantics_embed ducksemantics_ground ducksemantics_parse ducksemantics_provider_generics ducksemantics_run ducksemantics_token_embed
Read an OBO ontology into graph relationsducksemantics_read_obo
Record source-grounded judgmentsducksemantics_record_judgments
DuckDB semantic graph schemaducksemantics_schema_sql
Semantic table namesducksemantics_tables
Construct token embedding rowsducksemantics_token_embedding_batch
Construct token embedding rows from a providerducksemantics_token_embedding_batch_from_provider
Wrap a token embedding function as a token providerducksemantics_token_embedding_provider
Tokenize source textducksemantics_tokens
Store embedding rows in DuckDBducksemantics_write_embeddings
Write ontology graph rowsducksemantics_write_graph
Write an OBO ontology into the graphducksemantics_write_obo
Store token embedding rows in DuckDBducksemantics_write_token_embeddings
Grounding-provider protocolDucksemanticsAnnotator
Embedding-provider protocolDucksemanticsEmbeddingProvider
Judgment-parser provider protocolDucksemanticsJudgmentParser
Prompt-runner provider protocolDucksemanticsPromptRunner
Token-embedding-provider protocolDucksemanticsTokenEmbeddingProvider