NEWS.md

In neurogenomics/HPOExplorer: Analysis and Visualisation of the Human Phenotype Ontology

HPOExplorer 1.0.3

New features

• Upgrade add_disease to use cached definitions.

Bug fixes

• Fix tests for make_phenos_dataframe.
• Deprecate hpo_api as the HPO API was deprecated in the 2.0.0 Release (https://hpo.jax.org/data/api).

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

neurogenomics/HPOExplorer documentation built on Aug. 24, 2024, 1:39 a.m.