Changelog

Source: NEWS.md

HPOExplorer 1.0.1

New features

• Add Issues templates

Bug fixes

• Fix tests:
  • gpt_annot_check
  • add_hpo_id
• Fix functions: gpt_annot_plot

HPOExplorer 1.0.0

New features

• MAJOR CHANGES: Switched from ontologyIndex to simona, which seems to be better written and has extensive analysis functions.
• MAJOR CHANGES: Moved most non-HPO data annotation to KnowledgeNets
  • Functions to assess disease or phenotype prevalence (https://github.com/neurogenomics/RareDiseasePrioritisation/issues/34)
    • get_prevalence_orphanet
    • get_prevalence_oard
  • Functions to assess the existence of models for phenotypes or diseases (https://github.com/neurogenomics/RareDiseasePrioritisation/issues/33)
    • map_upheno
    • map_upheno_data
    • map_upheno_plots
    • map_upheno_heatmap
    • map_upheno_rainplot
    • map_upheno_scatterplot
    • get_monarch
    • get_monarch_models
• New exported functions:
  • Helper functions:
    • convert_hpo
  • Functions to map IDs across ontologies:
    • add_medgen
    • add_omop
    • add_prevalence
    • add_prevalence_report
• New internal functions:
  • dt_to_matrix

Bug fixes

• add_mondo
  • Drastically improved cross-ontology mappings to MONDO (https://github.com/monarch-initiative/mondo/issues/6873)
    • Add subfunction map_mondo

HPOExplorer 0.99.12

New features

• get_hpo
  • Updated to latest release: 2023-08-01
• gpt_annot_*
  • Ensure consistent use of updated column names.
• Add version attribute data within HPO objects
  • get_hpo: already built in to ontologyIndex objects.
  • load_phenotypes_to_genes: new attribute.
  • New exported helper function: get_version
  • New exported helper function: clear_cache
• Add make_ontology internal function.
• Ensure consistent function naming:
  • create_node_data –> make_node_data
• get_gencc
  • Export
  • Add version info
• Increase code coverage throughout

HPOExplorer 0.99.11

New features

• New GPT annotation functions
  • gpt_annot_read
  • gpt_annot_check
  • gpt_annot_codify
  • gpt_annot_plot
• get_hpo
  • Get OBO directly from “https://github.com/obophenotype/human-phenotype-ontology/releases” rather than Bioportal.
  • Used “hp-base.obo” as this seemed to match the file size of the OBO on Bioportal.
  • Also tried importing “hp-full.obo” but this caused an error with ontologyIndex::get_OBO.

Bug fixes

• load_phenotype_to_genes:
  • Revamp to use releases from “https://github.com/obophenotype/human-phenotype-ontology/releases”, which HPO now redirects to.
  • Use piggyback to download files.
• test-get_ont_lvls
  • New HPO has extra “GO:” terms. Omit them in tests.
• example_phenos
  • New HPO has extra “GO:” terms. Omit.

HPOExplorer 0.99.10

New features

• load_phenotype_to_genes
  • Update to use new annotation files.
• Switch terms:
  • “HPO_ID” –> “hpo_id”
  • “Phenotype” –> “hpo_name”
  • “FREQUENCY” –> “gene_freq”
  • “Onset” –> “onset”
  • “Modifier” –> “modifier”
  • “Aspect” –> “aspect”
  • “Gene” –> “gene_symbol”
  • “LinkID” –> “disease_id”
• Update all “data” objects.
• Update hpo object to “2023-06-17” release.

Bug fixes

• allow.cartesion –> allow.cartesian
• Document all args.
• add_onset
  • Circumvent Inf warnings.

HPOExplorer 0.99.9

New features

• load_phenotype_to_genes
  • Temporary fix while the HPO annotations are being fixed (they accidentally uploaded a version without the LinkIDs): use old files which I’ve uploaded copies of to GitHub Releases.
• get_gene_lengths
  • Turn off seqnames filter when keep_seqnames=NULL.
• New function: add_genes
  • Extracted from phenos_to_granges code.

Bug fixes

• phenos_to_granges
  • Make sure phenotype_to_genes is unique before.
  • Make sure there is only one gene length per gene symbol.
• add_disease
  • Make sure annot <- load_phenotype_to_genes(3) only has one entry per hpo_id/disease_id combination.

HPOExplorer 0.99.8

New features

• HPO data
  • Update from Bioportal: 2023-04-05
  • Recreate HPO with extract_tags = "everything".
  • Now includes useful tags like xref to get HPO ID mappings with other databases (MESH, SNOMED, UMLS).
  • store in Releases via piggyback to reduce package size.
• MONDO data
  • Create updated ontology_index obj and store in Releases.
  • New func: get_mondo
  • Now includes useful tags like xref to get HPO ID mappings with other databases (DOID, MESH, ICD9, GARD, EFO, SCTID, NCIT UMLS, Orphanet).
• get_data
  • New internal support func to get piggyback data.
• hpo_meta
  • Remove as this information is now stored within new hpo tags: hpo$def, hpo$xref, etc.

Bug fixes

• Update/simplify HPOExplorer vignette.

HPOExplorer 0.99.7

New features

• prioritise_targets
  • Move filtering steps and arg docs inside respective HPOExplorer::add_* functions.
• New funcs:
  • add_ndisease
  • add_disease_definition

Bug fixes

• De-aggregate add_* functions so that everything occurs at the level of “disease_id” + “hpo_id”.
• Remove Roxygen links to MultiEWCE

HPOExplorer 0.99.6

New features

• New function for creating gene x phenotype matrix
  • hpo_to_matrix

Bug fixes

• Add R.utils as Suggest.

HPOExplorer 0.99.5

New features

• New functions:
  • make_igraph_network
  • network_3d
  • kde_surface
• make_network_object: Now takes additional arguments to control the network layout.

HPOExplorer 0.99.4

New features

• example_phenos:
  • Simplified and fast
  • Used in all applicable examples.
• Create new hpo object:
  • This updates the HPO from 2016 (distributed by ontologyIndex) with an updated one from 2023.
  • Updated all data objects in HPOExplorer that may have relied on hpo to be generated.
• fix_hpo_ids
• New function for fixing issues with missing HPO IDs.

Bug fixes

• hpo_tiers:
  • Found lots of typos, outdated phenotype names, and mismatched HPO IDs. We through and manually re-curated all of these and checked that they match up with the map_phenotypes output.
  • Add original hpo_tiers csv to inst/extdata.
• Delete get_hpo_id function in favor of get_hpo_id_direct which is more reliable and comprehensive.

HPOExplorer 0.99.3

Bug fixes

• get_ont_lvls:
  • Worked w Bobby to clarify the role of each ontology level function.
  • Added new internal function to get the max ontology level: get_max_ont_lvl
  • Rewrote function description to make the differences between absolute/relative level more clear.
• make_network_object:
  • Use list_columns so that ontLvl_relative gets added to network obj.
• list_columns
• Add new arg extra_cols

HPOExplorer 0.99.2

New features

• Automatically load hpo with new func: get_hpo()
• Remove wesanderson from deps.
• Add remaining functions from rare_disease_celltyping_apps.
• Remove unused functions:
  • make_hoverbox
  • get_disease_description_dataframe
• Add hpo_tiers data from Momoko’s thesis.
• Make make_phenos_dataframe far more efficient.
• adjacency_matrix:
  • Simply turn into a shallow wrapper for nearly identical function: ontologyIndex::get_term_descendancy_matrix
• load_phenotype_to_genes:
  • Can now downlaod either phenotypes_to_genes or genes_to_phenotypes.
• New functions supporting gene target prioritisation:
  • phenos_to_granges
  • add_onset
  • add_tier
  • map_phenotypes
  • get_gene_lists
  • get_gene_lengths
  • list_onsets

Bug fixes

• Remove globals.R.
• Avoid redundancy with:
  • get_relative_ont_level ~= find_parent ~= get_ont_level –> get_ont_lvl
  • get_relative_ont_level_multiple ~= get_hierarchy –> get_ont_lvls

HPOExplorer 0.99.2

New features

• Added a NEWS.md file to track changes to the package.
• Implemented rworkflows
• make_network_plot: make interactive with plotly
• Add simplifying wrapper functions:
  • make_hoverboxes
  • make_phenos_dataframe
• Add verbose arg throughout.
• Cache file from load_phenotype_to_genes
• Add hpo_meta data to speed everything up.
  • Add helper func to preprocess data: as_ascii

Bug fixes

• Make examples runnable.
• Fix Imports
• Update and streamline Get started vignette.
• Remove unused functions:
  • download_phenotype_to_genes
  • hpo_term_definition_list