Make species first class supported (1/2)

[Zethson]

Task summary of a discussion between @sunnyosun and me

new current/lndb

Species:
  all:
    ensembl: release-108
Gene:
  human:
    ensembl: release-108
  mouse:
    ensembl: release-108
Protein:
  all:
    uniprot: 2022-04
CellMarker:
  all:
    cellmarker: '2.0'
CellLine:
    all:
  clo: '2022-03-21'
CellType:
  all:
    cl: '2023-02-15'
Tissue:
  all:
    uberon: '2023-02-14'
Disease:
  all:
    mondo: '2023-02-06'
Readout:
  all:
    efo: 3.48.0
Phenotype:
  human:
    hp: '2023-01-27'
Pathway:
  all:
    pw: 7.74
Drug:
  all:
    dron: '2023-03-10'
BFXPipeline:
  all:
    lamin: 1.0.0

new versions/local

version: "0.2.0"
Species:
  ensembl:
    versions:
      release-108:
        source: https://ftp.ensembl.org/pub/release-108/mysql/
        md5: ""
    species:
      - all
    name: Ensembl
    website: https://www.ensembl.org/index.html
Gene:
  ensembl:
    versions:
      release-108:
        source: https://ftp.ensembl.org/pub/release-108/mysql/
        md5: ""
      release-107:
        source: https://ftp.ensembl.org/pub/release-107/mysql/
        md5: ""
    species:
      - human
      - mouse
    name: Ensembl
    website: https://www.ensembl.org/index.html
Protein:
  uniprot:
    versions:
      2022-04:
        source: https://ftp.uniprot.org/pub/databases/uniprot/current_release/
        md5: ""
      2022-03:
        source: https://ftp.uniprot.org/pub/databases/uniprot/previous_releases/release-2022_03/
        md5: ""
    species:
      - all
    name: Uniprot
    website: https://www.uniprot.org/
CellMarker:
  cellmarker:
    versions:
      2.0:
        source: http://bio-bigdata.hrbmu.edu.cn/CellMarker/CellMarker_download_files/file/Cell_marker_All.xlsx
        md5: ""
    species:
      - all
    name: CellMarker
    website: http://bio-bigdata.hrbmu.edu.cn/CellMarker/
CellLine:
  clo:
    versions:
      2022-03-21:
        source: https://data.bioontology.org/ontologies/CLO/submissions/65/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb
        md5: ea58a1010b7e745702a8397a526b3a33
    species:
      - all
    name: Cell Line Ontology
    website: https://bioportal.bioontology.org/ontologies/CLO
CellType:
  cl:
    versions:
      2023-02-15:
        source: http://purl.obolibrary.org/obo/cl/releases/2023-02-15/cl-base.owl
        md5: 9331a6a029cb1863bd0584ab41508df7
      2022-08-16:
        source: http://purl.obolibrary.org/obo/cl/releases/2022-08-16/cl.owl
        md5: d0655766574e63f3fe5ed56d3c030880
    species:
      - all
    name: Cell Ontology
    website: https://obophenotype.github.io/cell-ontology/
Tissue:
  uberon:
    versions:
      2023-02-14:
        source: http://purl.obolibrary.org/obo/uberon/releases/2023-02-14/uberon.owl
        md5: 3f94e22fae4cdde88a555c5cd59c47da
      2022-08-19:
        source: http://purl.obolibrary.org/obo/uberon/releases/2022-08-19/uberon.owl
        md5: c7c958a1ee48fdce146f2c1763eed27e
    species:
      - all
    name: Uberon multi-species anatomy ontology
    website: http://obophenotype.github.io/uberon/
Disease:
  mondo:
    versions:
      2023-02-06:
        source: http://purl.obolibrary.org/obo/mondo/releases/2023-02-06/mondo.owl
        md5: 2b7d479d4bd02a94eab47d1c9e64c5db
      2022-10-11:
        source: http://purl.obolibrary.org/obo/mondo/releases/2022-10-11/mondo.owl
        md5: 04b808d05c2c2e81430b20a0e87552bb
    name: Mondo Disease Ontology
    website: https://mondo.monarchinitiative.org/
  doid:
    versions:
      2023-01-30:
        source: http://purl.obolibrary.org/obo/doid/releases/2023-01-30/doid.obo
        md5: 9f0c92ad2896dda82195e9226a06dc36
    species:
      - human
    name: Human Disease Ontology
    website: https://disease-ontology.org/
Readout:
  efo:
    versions:
      3.48.0:
        source: http://www.ebi.ac.uk/efo/releases/v3.48.0/efo.owl
        md5: 3367e9a9ae3dee9113024e5108c49091
    species:
      - all
    name: The Experimental Factor Ontology
    website: https://bioportal.bioontology.org/ontologies/EFO
Phenotype:
  hp:
    versions:
      2023-01-27:
        source: https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2023-01-27/hp.owl
        md5: ceeb3ada771908deef620d74cd8e6b0f
    species:
      - human
    name: Human Phenotype Ontology
    website: https://hpo.jax.org/
Pathway:
  go:
    versions:
      2023-05-10:
        source: https://data.bioontology.org/ontologies/GO/submissions/1814/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb
        md5: ""
    species:
      - all
    name: Gene Ontology
    website: http://geneontology.org/docs/download-ontology/
  pw:
    versions:
      7.78:
        source: https://data.bioontology.org/ontologies/PW/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb&download_format=rdf
        md5: a6df86616149dcdfe08fe16c900cba85
    species:
      - all
    name: Pathway Ontology
    website: https://www.ebi.ac.uk/ols/ontologies/pw
BFXPipeline:
  lamin:
    versions:
      1.0.0:
        source: s3://bionty-assets/bfxpipelines.json
        md5: ""
    species:
      - all
    name: Bioinformatics Pipeline
    website: https://lamin.ai
Drug:
  dron:
    versions:
      2023-03-10:
        source: https://data.bioontology.org/ontologies/DRON/submissions/17/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb
        md5: ""
    species:
      - all
    name: Drug Ontology
    website: https://bioportal.bioontology.org/ontologies/DRON/?p=summary

• [x] Adapt the versions.yaml file structure to also include species
• [x] Ensure that the local.yaml is properly created
• [x] Ensure that the current.yaml and lndb.yaml are properly created
• [x] Fix the local/current diff
• [x] Fix update defaults
• [x] Ensure tests is running
• [x] Now load in things and ensure that Bionty still works
• [x] Adapt display stuff
• [x] Ask users to regenerate their yaml files when an older yaml version is detected. Provide instructions on how to do it.
• [x] Another thing that bothered me a bit when passing species in downstream functionalities in lamindb and lnschema-bionty is, the default value. I had to specifically not pass “species” in order to make sure default value is used. So could we just have the species=None as the default? and assign “all” or “human” within the init?

[sunnyosun]

Currently, there's a design flaw that if users pass a random species, for instance bt.Tissue(species='mouse') will trigger downloading ontology file from the original source with name prefixed with mouse__. This should be resolved after the new design.