# GOSemSim 2.39.2

+ add `set_auto_update()` to control auto-update of ontology databases (2026-06-29, Mon)

# GOSemSim 2.39.1

+ improve pairwise similarity performance by reducing repeated matrix scans in score combination (2026-06-28, Sun)
+ support optional `BiocParallel` parallel pairwise calculation in `mgeneSim()` and `mclusterSim()` (#31, 2026-06-28, Sun)
+ improve TCSS robustness and document TCSS usage with topology cutoff preprocessing (2026-06-28, Sun)
+ fix Wang method semantic value cache to avoid reusing GO term values across ontologies (#30, 2026-06-28, Sun)
+ fix Wang method edge weighting for GO relationships by normalizing `isa` and `part of` relationship names (#51, 2026-06-28, Sun)

# GOSemSim 2.38.0

+ Bioconductor RELEASE_3_23 (2026-04-29, Wed)

# GOSemSim 2.37.2

+ refactor `.initial()` to use a controlled environment for robust data loading (2026-01-15, Thu)
+ enhance cache reading robustness in `computeIC()` and `wangMethod_internal()` (2026-01-15, Thu)
+ update `load_onto()` documentation (2026-01-12, Mon)
+ enhance `godata()` input validation (2026-01-12, Mon)
+ refactor internal ontology type checking (2026-01-12, Mon)
+ fix cache integration in `.initial` and refactor consumers to use `get_cache_element` (2026-01-12, Mon)
+ fix `load_onto()` using cache incorrectly (2026-01-12, Mon)
+ use cache mechanisms defined in 'yulab.utils' for caching (2026-01-12, Mon) 
+ update URLs, fix typos and refine roxygen documentation (2026-01-12, Mon)

# GOSemSim 2.37.1

+ use cache mechanisms defined in 'yulab.utils' for caching (2025-12-08, Mon) 
+ update roxygen to use 'markdown' syntax and unify duplicated docs into templates (in 'man-roxygen' folder) (2025-12-07, Sun)
+ move `get_organism()` from 'DOSE' (2025-12-07, Sun)
+ move `load_OrgDb()` to 'yulab.utils' (2025-12-05, Fri)

# GOSemSim 2.36.0

+ Bioconductor RELEASE_3_22 (2025-11-01, Sat)

# GOSemSim 2.35.2

+ bug fixed that introduced in previous commit (2025-10-03, Fri)
  - <https://github.com/YuLab-SMU/DOSE/issues/86#issuecomment-3361787836>

# GOSemSim 2.35.1

+ alternative url for `load_onto()` (2025-08-12, Tue)

# GOSemSim 2.34.0

+ Bioconductor RELEASE_3_21 (2025-04-17, Thu)

# GOSemSim 2.32.0

+ Bioconductor RELEASE_3_20 (2024-10-30, Wed)

# GOSemSim 2.31.1

+ `get_rel_df()` to access ontology relation data frame required by the Wang method (2024-08-13, Tue)
+ a set of 'OntDb' methods for accessing sqlite data generated by the 'obolite' package (2024-08-13, Tue)
+ use `yulab.utils::yulab_msg()` for startup message (2024-07-26, Fri)

# GOSemSim 2.30.0

+ Bioconductor RELEASE_3_19 (2024-05-15, Wed)

# GOSemSim 2.29.2

+ update `buildGOmap()` parameter to be consistent with `enricher()` and `GSEA()` (2024-02-06, Tue, #47)

# GOSemSim 2.29.1

+ extend `godata()` to support passing a data.frame (can be output of `read.gaf()` or `read.blast2go()`) to 'annoDb' (2023-01-16, Tue)
+ deprecate 'OrgDb' and introduce new parameter 'annoDb' in `godata()` 
+ standardize the output of `read.gaf()` and `read.blast2go()`
+ optimize `buildGOmap()`

# GOSemSim 2.28.0

+ Bioconductor RELEASE_3_18 (2023-10-25, Wed)

# GOSemSim 2.27.3

+ use `check_installed()` to check package dependency (2023-09-12, Tue, #43)

# GOSemSim 2.27.2

+ `read.blast2go()` to parse 'blast2go' result (2023-07-10, Mon, #41, #42)
+ move `buildGOmap()` and `read.gaf()` from 'clusterProfiler' (2023-07-10, Mon)

# GOSemSim 2.27.1

+ semantic similarity measurement support for MPO (2023-04-06, Thu)
+ TCSS semantic similarity measurement support for DO and MPO (2023-04-06, Thu)

# GOSemSim 2.26.0

+ Bioconductor RELEASE_3_17 (2023-05-03, Wed)

# GOSemSim 2.24.0

+ Bioconductor RELEASE_3_16 (2022-11-02, Wed)

# GOSemSim 2.23.1

+ Replacing DO.db with HDO.db (2022-07-29, Mon)

# GOSemSim 2.22.0

+ Bioconductor 3.15 release

# GOSemSim 2.21.1

+ Avoid eval-parse in `load_OrgDb()` (2022-01-10, Mon)

# GOSemSim 2.20

+ Bioconductor 3.14 release

# GOSemSim 2.19.1

+ TCSS method (@qibaiqi, #35; 2021-08-02, Mon)

# GOSemSim 2.18.0

+ Bioconductor 3.13 release

# GOSemSim 2.17.1

+ bug fixed according to the update of GO.db (2020-10-29, Thu)
  - <https://github.com/YuLab-SMU/GOSemSim/issues/32>
  
# GOSemSim 2.16.0

+ Bioconductor 3.12 release (2020-10-28, Wed)

# GOSemSim 2.15.2

+ new site, <https://yulab-smu.top/biomedical-knowledge-mining-book/> for documentation (2020-09-04, Fri)
+ update vignette
+ update `data/gotbl`

# GOSemSim 2.15.1

+ bug fixed of IC method when input IDs contain invalid terms. (2020-07-25, Sat)

# GOSemSim 2.14.0

+ Bioconductor 3.11 release


# GOSemSim 2.13.1

+ add new citation (2020-03-19, Thu)
+ fixed compiling error due to the change of Rcpp 
  - <https://github.com/YuLab-SMU/GOSemSim/issues/27>

# GOSemSim 2.7.1

+ `mgeneSim` and `mclusterSim` now always return matrix (2018-08-08, Wed)
    - <https://www.biostars.org/p/330642/#331598>

# GOSemSim 2.5.1

+ return NA for deprecated IDs (2018-01-09, Fri)
    - <https://support.bioconductor.org/p/105822/#105840>
