Update data links and sources in EXTERNAL_DATA.md - #24
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Pull request overview
Updates the pixi_phenotype_score module’s external data manifest to reflect current dataset versions and provide more actionable acquisition information for required third-party resources.
Changes:
- Renames the table column from “目标路径” to “数据链接” and switches several entries from local paths to upstream download URLs.
- Updates dataset version/date metadata for HGNC and Orphapackets.
- Clarifies OMIM acquisition constraints by indicating it must be obtained via OMIM registration.
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| | Orphapackets | 当前部署批次 | 60 MB | 索引缺失时需要 | `external_data/orphanet/Orphapackets/` | [Orphadata](https://www.orphadata.com/) | | ||
| | Orphanet gene profile index | 由 Orphapackets 派生 | 9.0 MB | 推荐 | `external_data/indexes/orpha_gene_profiles.pkl` | 本项目生成 | | ||
| | HPO ontology | 2026-02-16 | 10.2 MB | 是 | `https://purl.obolibrary.org/obo/hp.obo` | [HPO official releases](https://github.com/obophenotype/human-phenotype-ontology/releases) | | ||
| | HPO disease annotations | 2026-02-16 | 33.6 MB | 是 | `http://purl.obolibrary.org/obo/hp/hpoa/phenotype.hpoa` | [HPO official releases](https://github.com/obophenotype/human-phenotype-ontology/releases) | |
| | Orphanet gene profile index | 由 Orphapackets 派生 | 9.0 MB | 推荐 | `external_data/indexes/orpha_gene_profiles.pkl` | 本项目生成 | | ||
| | HPO ontology | 2026-02-16 | 10.2 MB | 是 | `https://purl.obolibrary.org/obo/hp.obo` | [HPO official releases](https://github.com/obophenotype/human-phenotype-ontology/releases) | | ||
| | HPO disease annotations | 2026-02-16 | 33.6 MB | 是 | `http://purl.obolibrary.org/obo/hp/hpoa/phenotype.hpoa` | [HPO official releases](https://github.com/obophenotype/human-phenotype-ontology/releases) | | ||
| | HPO gene-disease associations | 2026-02-16 | 1.4 MB | 是 | `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_disease.txt` | [HPO GitHub releases](https://github.com/obophenotype/human-phenotype-ontology/releases) | |
| | HPO ontology | 2026-02-16 | 10.2 MB | 是 | `https://purl.obolibrary.org/obo/hp.obo` | [HPO official releases](https://github.com/obophenotype/human-phenotype-ontology/releases) | | ||
| | HPO disease annotations | 2026-02-16 | 33.6 MB | 是 | `http://purl.obolibrary.org/obo/hp/hpoa/phenotype.hpoa` | [HPO official releases](https://github.com/obophenotype/human-phenotype-ontology/releases) | | ||
| | HPO gene-disease associations | 2026-02-16 | 1.4 MB | 是 | `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_disease.txt` | [HPO GitHub releases](https://github.com/obophenotype/human-phenotype-ontology/releases) | | ||
| | HGNC complete set | 2026-05-27 | 16.0 MB | 是 | `https://storage.googleapis.com/public-download-files/hgnc/tsv/tsv/hgnc_complete_set.txt` | [HGNC downloads](https://www.genenames.org/download/custom/) | |
| | HPO disease annotations | 2026-02-16 | 33.6 MB | 是 | `http://purl.obolibrary.org/obo/hp/hpoa/phenotype.hpoa` | [HPO official releases](https://github.com/obophenotype/human-phenotype-ontology/releases) | | ||
| | HPO gene-disease associations | 2026-02-16 | 1.4 MB | 是 | `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_disease.txt` | [HPO GitHub releases](https://github.com/obophenotype/human-phenotype-ontology/releases) | | ||
| | HGNC complete set | 2026-05-27 | 16.0 MB | 是 | `https://storage.googleapis.com/public-download-files/hgnc/tsv/tsv/hgnc_complete_set.txt` | [HGNC downloads](https://www.genenames.org/download/custom/) | | ||
| | MONDO rare subset | 2026-05-05 | 31.8 MB | 是 | `http://purl.obolibrary.org/obo/mondo/subsets/mondo-rare.obo` | [MONDO downloads](https://mondo.monarchinitiative.org/pages/download/) | |
| | HGNC complete set | 2026-05-27 | 16.0 MB | 是 | `https://storage.googleapis.com/public-download-files/hgnc/tsv/tsv/hgnc_complete_set.txt` | [HGNC downloads](https://www.genenames.org/download/custom/) | | ||
| | MONDO rare subset | 2026-05-05 | 31.8 MB | 是 | `http://purl.obolibrary.org/obo/mondo/subsets/mondo-rare.obo` | [MONDO downloads](https://mondo.monarchinitiative.org/pages/download/) | | ||
| | OMIM SQLite | 2025-04-11 | 311.6 MB | 是 | `需OMIM注册获取` | [OMIM downloads](https://www.omim.org/downloads/) | | ||
| | Orphapackets | 2026-05-29 | 60 MB | 是 | `https://github.com/Orphanet/orphapacket/tree/master/yaml` | [Orphadata](https://www.orphadata.com/) | |
OpenRare2026
approved these changes
Jul 10, 2026
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