Developmental stage#
lamindb provides access to the following public developmental stage ontologies through lnschema-bionty:
Here we show how to access and search developmental stage ontologies to standardize new data.
Setup#
!lamin init --storage ./test-developmental-stage --schema bionty
✅ saved: User(uid='DzTjkKse', handle='testuser1', name='Test User1', updated_at=2024-01-07 21:26:16 UTC)
✅ saved: Storage(uid='La9Dy7IX', root='/home/runner/work/lamin-usecases/lamin-usecases/docs/test-developmental-stage', type='local', updated_at=2024-01-07 21:26:16 UTC, created_by_id=1)
💡 loaded instance: testuser1/test-developmental-stage
💡 did not register local instance on hub
import lnschema_bionty as lb
import pandas as pd
# adds an entry "human" into an empty instance
lb.settings.organism = "human"
💡 loaded instance: testuser1/test-developmental-stage
Bionty objects#
Let us create a public knowledge accessor with bionty(), which chooses a default public knowledge source from BiontySource. It’s a Bionty object, which you can think about as a less-capable registry:
developmental_stage_bt = lb.DevelopmentalStage.bionty()
developmental_stage_bt
DevelopmentalStage
Organism: human
Source: hsapdv, 2020-03-10
#terms: 243
📖 DevelopmentalStage.df(): ontology reference table
🔎 DevelopmentalStage.lookup(): autocompletion of terms
🎯 DevelopmentalStage.search(): free text search of terms
✅ DevelopmentalStage.validate(): strictly validate values
🧐 DevelopmentalStage.inspect(): full inspection of values
👽 DevelopmentalStage.standardize(): convert to standardized names
🪜 DevelopmentalStage.diff(): difference between two versions
🔗 DevelopmentalStage.ontology: Pronto.Ontology object
As for registries, you can export the ontology as a DataFrame:
df = developmental_stage_bt.df()
df.head()
| name | definition | synonyms | parents | |
|---|---|---|---|---|
| ontology_id | ||||
| HsapDv:0000000 | human life cycle stage | A Spatiotemporal Region Encompassing Some Part... | developmental stage | [] |
| HsapDv:0000001 | human life cycle | Temporal Interval That Defines Human Life From... | None | [HsapDv:0000000] |
| HsapDv:0000002 | embryonic human stage | Prenatal Stage That Starts With Fertilization ... | None | [HsapDv:0000000] |
| HsapDv:0000003 | Carnegie stage 01 | Embryonic Stage Defined By A Fertilized Oocyte... | CS01 | [HsapDv:0000000] |
| HsapDv:0000004 | cleavage stage | Early Stage Of Carnegie Stage 02 Consisting Of... | None | [HsapDv:0000000] |
Unlike registries, you can also export it as a Pronto object via developmental_stage_bt.ontology.
Look up terms#
As for registries, terms can be looked up with auto-complete:
lookup = developmental_stage_bt.lookup()
The . accessor provides normalized terms (lower case, only contains alphanumeric characters and underscores):
lookup.organogenesis_stage
DevelopmentalStage(ontology_id='HsapDv:0000015', name='organogenesis stage', definition='Embryonic Stage At Which The Ectoderm, Endoderm, And Mesoderm Develop Into The Internal Organs Of The Organism.', synonyms=None, parents=array(['HsapDv:0000000'], dtype=object))
To look up the exact original strings, convert the lookup object to dict and use the [] accessor:
lookup_dict = lookup.dict()
lookup_dict["organogenesis stage"]
DevelopmentalStage(ontology_id='HsapDv:0000015', name='organogenesis stage', definition='Embryonic Stage At Which The Ectoderm, Endoderm, And Mesoderm Develop Into The Internal Organs Of The Organism.', synonyms=None, parents=array(['HsapDv:0000000'], dtype=object))
By default, the name field is used to generate lookup keys. You can specify another field to look up:
lookup = developmental_stage_bt.lookup(developmental_stage_bt.ontology_id)
If multiple entries are matched, they are returned as a list:
lookup.hsapdv_0000015
DevelopmentalStage(ontology_id='HsapDv:0000015', name='organogenesis stage', definition='Embryonic Stage At Which The Ectoderm, Endoderm, And Mesoderm Develop Into The Internal Organs Of The Organism.', synonyms=None, parents=array(['HsapDv:0000000'], dtype=object))
Search terms#
Search behaves in the same way as it does for registries:
developmental_stage_bt = lb.DevelopmentalStage.bionty()
developmental_stage_bt.search("organogenesis").head(3)
| ontology_id | definition | synonyms | parents | __ratio__ | |
|---|---|---|---|---|---|
| name | |||||
| organogenesis stage | HsapDv:0000015 | Embryonic Stage At Which The Ectoderm, Endoder... | None | [HsapDv:0000000] | 95.000000 |
| morula stage | HsapDv:0000205 | The Morula Stage Is The Later Part Of Carnegie... | None | [HsapDv:0000000] | 40.000000 |
| 80 year-old and over human stage | HsapDv:0000095 | Aged Stage That Refers To An Adult Who Is Over... | None | [HsapDv:0000000] | 39.461538 |
By default, search also covers synonyms:
developmental_stage_bt.search("developmental stage").head(3)
| ontology_id | definition | synonyms | parents | __ratio__ | |
|---|---|---|---|---|---|
| name | |||||
| human life cycle stage | HsapDv:0000000 | A Spatiotemporal Region Encompassing Some Part... | developmental stage | [] | 100.000000 |
| prenatal stage | HsapDv:0000045 | Prenatal Stage That Starts With Fertilization ... | None | [HsapDv:0000000] | 72.727273 |
| fetal stage | HsapDv:0000037 | Prenatal Stage That Starts With The Fully Form... | None | [HsapDv:0000000] | 66.666667 |
Standardize developmental stage identifiers#
Let us generate a DataFrame that stores a number of disease identifiers, some of which corrupted:
df_orig = pd.DataFrame(
index=[
"blastula stage",
"Carnegie stage 03",
"neurula stage",
"organogenesis stage",
"This developmental stage does not exist",
]
)
df_orig
| blastula stage |
|---|
| Carnegie stage 03 |
| neurula stage |
| organogenesis stage |
| This developmental stage does not exist |
We can check whether any of our values are validated against the ontology reference:
validated = developmental_stage_bt.validate(df_orig.index, developmental_stage_bt.name)
df_orig.index[~validated]
❗ 1 term (20.00%) is not validated: This developmental stage does not exist
Index(['This developmental stage does not exist'], dtype='object')
Ontology source versions#
For any given entity, we can choose from a number of versions:
lb.BiontySource.filter(entity="DevelopmentalStage").df()
| uid | entity | organism | currently_used | source | source_name | version | url | md5 | source_website | created_at | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||
| 48 | 7JhT | DevelopmentalStage | human | True | hsapdv | Human Developmental Stages | 2020-03-10 | http://aber-owl.net/media/ontologies/HSAPDV/11... | 52181d59df84578ed69214a5cb614036 | https://github.com/obophenotype/developmental-... | 2024-01-07 21:26:16.913885+00:00 | 2024-01-07 21:26:16.913894+00:00 | 1 |
| 49 | JIKv | DevelopmentalStage | mouse | True | mmusdv | Mouse Developmental Stages | 2020-03-10 | http://aber-owl.net/media/ontologies/MMUSDV/9/... | 5bef72395d853c7f65450e6c2a1fc653 | https://github.com/obophenotype/developmental-... | 2024-01-07 21:26:16.913985+00:00 | 2024-01-07 21:26:16.913994+00:00 | 1 |
When instantiating a Bionty object, we can choose a source or version:
bionty_source = lb.BiontySource.filter(
source="hsapdv", version="2020-03-10", organism="human"
).one()
developmental_stage_bt = lb.DevelopmentalStage.bionty(bionty_source=bionty_source)
developmental_stage_bt
DevelopmentalStage
Organism: human
Source: hsapdv, 2020-03-10
#terms: 243
📖 DevelopmentalStage.df(): ontology reference table
🔎 DevelopmentalStage.lookup(): autocompletion of terms
🎯 DevelopmentalStage.search(): free text search of terms
✅ DevelopmentalStage.validate(): strictly validate values
🧐 DevelopmentalStage.inspect(): full inspection of values
👽 DevelopmentalStage.standardize(): convert to standardized names
🪜 DevelopmentalStage.diff(): difference between two versions
🔗 DevelopmentalStage.ontology: Pronto.Ontology object
The currently used ontologies can be displayed using:
lb.BiontySource.filter(currently_used=True).df()
| uid | entity | organism | currently_used | source | source_name | version | url | md5 | source_website | created_at | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||
| 1 | zvGR | Organism | vertebrates | True | ensembl | Ensembl | release-110 | https://ftp.ensembl.org/pub/release-110/specie... | f3faf95648d3a2b50fd3625456739706 | https://www.ensembl.org | 2024-01-07 21:26:16.909064+00:00 | 2024-01-07 21:26:16.909083+00:00 | 1 |
| 4 | TE9h | Organism | bacteria | True | ensembl | Ensembl | release-57 | https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... | ee28510ed5586ea7ab4495717c96efc8 | https://www.ensembl.org | 2024-01-07 21:26:16.909411+00:00 | 2024-01-07 21:26:16.909420+00:00 | 1 |
| 5 | OZIG | Organism | fungi | True | ensembl | Ensembl | release-57 | http://ftp.ensemblgenomes.org/pub/fungi/releas... | dbcde58f4396ab8b2480f7fe9f83df8a | https://www.ensembl.org | 2024-01-07 21:26:16.909513+00:00 | 2024-01-07 21:26:16.909522+00:00 | 1 |
| 6 | W07m | Organism | metazoa | True | ensembl | Ensembl | release-57 | http://ftp.ensemblgenomes.org/pub/metazoa/rele... | 424636a574fec078a61cbdddb05f9132 | https://www.ensembl.org | 2024-01-07 21:26:16.909614+00:00 | 2024-01-07 21:26:16.909624+00:00 | 1 |
| 7 | AVh3 | Organism | plants | True | ensembl | Ensembl | release-57 | https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... | eadaa1f3e527e4c3940c90c7fa5c8bf4 | https://www.ensembl.org | 2024-01-07 21:26:16.909714+00:00 | 2024-01-07 21:26:16.909724+00:00 | 1 |
| 8 | MdBu | Organism | all | True | ncbitaxon | NCBItaxon Ontology | 2023-06-20 | s3://bionty-assets/df_all__ncbitaxon__2023-06-... | 00d97ba65627f1cd65636d2df22ea76c | https://github.com/obophenotype/ncbitaxon | 2024-01-07 21:26:16.909814+00:00 | 2024-01-07 21:26:16.909824+00:00 | 1 |
| 9 | o36k | Gene | human | True | ensembl | Ensembl | release-110 | s3://bionty-assets/df_human__ensembl__release-... | 832f3947e83664588d419608a469b528 | https://www.ensembl.org | 2024-01-07 21:26:16.909914+00:00 | 2024-01-07 21:26:16.909924+00:00 | 1 |
| 11 | VTEw | Gene | mouse | True | ensembl | Ensembl | release-110 | s3://bionty-assets/df_mouse__ensembl__release-... | fa4ce130f2929aefd7ac3bc8eaf0c4de | https://www.ensembl.org | 2024-01-07 21:26:16.910117+00:00 | 2024-01-07 21:26:16.910127+00:00 | 1 |
| 13 | Uhnp | Gene | saccharomyces cerevisiae | True | ensembl | Ensembl | release-110 | s3://bionty-assets/df_saccharomyces cerevisiae... | 2e59495a3e87ea6575e408697dd73459 | https://www.ensembl.org | 2024-01-07 21:26:16.910323+00:00 | 2024-01-07 21:26:16.910333+00:00 | 1 |
| 14 | 000Q | Protein | human | True | uniprot | Uniprot | 2023-03 | s3://bionty-assets/df_human__uniprot__2023-03_... | 1c46e85c6faf5eff3de5b4e1e4edc4d3 | https://www.uniprot.org | 2024-01-07 21:26:16.910432+00:00 | 2024-01-07 21:26:16.910443+00:00 | 1 |
| 16 | tD7O | Protein | mouse | True | uniprot | Uniprot | 2023-03 | s3://bionty-assets/df_mouse__uniprot__2023-03_... | 9d5e9a8225011d3218e10f9bbb96a46c | https://www.uniprot.org | 2024-01-07 21:26:16.910639+00:00 | 2024-01-07 21:26:16.910648+00:00 | 1 |
| 18 | vqWI | CellMarker | human | True | cellmarker | CellMarker | 2.0 | s3://bionty-assets/human_cellmarker_2.0_CellMa... | d565d4a542a5c7e7a06255975358e4f4 | http://bio-bigdata.hrbmu.edu.cn/CellMarker | 2024-01-07 21:26:16.910845+00:00 | 2024-01-07 21:26:16.910855+00:00 | 1 |
| 19 | ypPK | CellMarker | mouse | True | cellmarker | CellMarker | 2.0 | s3://bionty-assets/mouse_cellmarker_2.0_CellMa... | 189586732c63be949e40dfa6a3636105 | http://bio-bigdata.hrbmu.edu.cn/CellMarker | 2024-01-07 21:26:16.910945+00:00 | 2024-01-07 21:26:16.910955+00:00 | 1 |
| 20 | 2Zjk | CellLine | all | True | clo | Cell Line Ontology | 2022-03-21 | https://data.bioontology.org/ontologies/CLO/su... | ea58a1010b7e745702a8397a526b3a33 | https://bioportal.bioontology.org/ontologies/CLO | 2024-01-07 21:26:16.911045+00:00 | 2024-01-07 21:26:16.911055+00:00 | 1 |
| 21 | 4shh | CellType | all | True | cl | Cell Ontology | 2023-08-24 | http://purl.obolibrary.org/obo/cl/releases/202... | 46e7dd89421f1255cf0191eca1548f73 | https://obophenotype.github.io/cell-ontology | 2024-01-07 21:26:16.911145+00:00 | 2024-01-07 21:26:16.911154+00:00 | 1 |
| 25 | LmWQ | Tissue | all | True | uberon | Uberon multi-species anatomy ontology | 2023-09-05 | http://purl.obolibrary.org/obo/uberon/releases... | abcee3ede566d1311d758b853ccdf5aa | http://obophenotype.github.io/uberon | 2024-01-07 21:26:16.911546+00:00 | 2024-01-07 21:26:16.911555+00:00 | 1 |
| 29 | zMWv | Disease | all | True | mondo | Mondo Disease Ontology | 2023-08-02 | http://purl.obolibrary.org/obo/mondo/releases/... | 7f33767422042eec29f08b501fc851db | https://mondo.monarchinitiative.org | 2024-01-07 21:26:16.911982+00:00 | 2024-01-07 21:26:16.911991+00:00 | 1 |
| 33 | cxPr | Disease | human | True | doid | Human Disease Ontology | 2023-03-31 | http://purl.obolibrary.org/obo/doid/releases/2... | 64f083a1e47867c307c8eae308afc3bb | https://disease-ontology.org | 2024-01-07 21:26:16.912388+00:00 | 2024-01-07 21:26:16.912397+00:00 | 1 |
| 35 | 2wto | ExperimentalFactor | all | True | efo | The Experimental Factor Ontology | 3.57.0 | http://www.ebi.ac.uk/efo/releases/v3.57.0/efo.owl | 2ecafc69b3aba7bdb31ad99438505c05 | https://bioportal.bioontology.org/ontologies/EFO | 2024-01-07 21:26:16.912587+00:00 | 2024-01-07 21:26:16.912596+00:00 | 1 |
| 37 | 3SSF | Phenotype | human | True | hp | Human Phenotype Ontology | 2023-06-17 | https://github.com/obophenotype/human-phenotyp... | 65e8d96bc81deb893163927063b10c06 | https://hpo.jax.org | 2024-01-07 21:26:16.912784+00:00 | 2024-01-07 21:26:16.912793+00:00 | 1 |
| 40 | nwdt | Phenotype | mammalian | True | mp | Mammalian Phenotype Ontology | 2023-05-31 | https://github.com/mgijax/mammalian-phenotype-... | be89052cf6d9c0b6197038fe347ef293 | https://github.com/mgijax/mammalian-phenotype-... | 2024-01-07 21:26:16.913081+00:00 | 2024-01-07 21:26:16.913090+00:00 | 1 |
| 41 | zAfB | Phenotype | zebrafish | True | zp | Zebrafish Phenotype Ontology | 2022-12-17 | https://github.com/obophenotype/zebrafish-phen... | 03430b567bf153216c0fa4c3440b3b24 | https://github.com/obophenotype/zebrafish-phen... | 2024-01-07 21:26:16.913184+00:00 | 2024-01-07 21:26:16.913198+00:00 | 1 |
| 43 | p1co | Phenotype | all | True | pato | Phenotype And Trait Ontology | 2023-05-18 | http://purl.obolibrary.org/obo/pato/releases/2... | bd472f4971492109493d4ad8a779a8dd | https://github.com/pato-ontology/pato | 2024-01-07 21:26:16.913387+00:00 | 2024-01-07 21:26:16.913396+00:00 | 1 |
| 44 | h0rU | Pathway | all | True | go | Gene Ontology | 2023-05-10 | https://data.bioontology.org/ontologies/GO/sub... | e9845499eadaef2418f464cd7e9ac92e | http://geneontology.org | 2024-01-07 21:26:16.913487+00:00 | 2024-01-07 21:26:16.913496+00:00 | 1 |
| 46 | fxHJ | BFXPipeline | all | True | lamin | Bioinformatics Pipeline | 1.0.0 | s3://bionty-assets/bfxpipelines.json | a7eff57a256994692fba46e0199ffc94 | https://lamin.ai | 2024-01-07 21:26:16.913686+00:00 | 2024-01-07 21:26:16.913695+00:00 | 1 |
| 47 | chfO | Drug | all | True | dron | Drug Ontology | 2023-03-10 | https://data.bioontology.org/ontologies/DRON/s... | 75e86011158fae76bb46d96662a33ba3 | https://bioportal.bioontology.org/ontologies/DRON | 2024-01-07 21:26:16.913786+00:00 | 2024-01-07 21:26:16.913795+00:00 | 1 |
| 48 | 7JhT | DevelopmentalStage | human | True | hsapdv | Human Developmental Stages | 2020-03-10 | http://aber-owl.net/media/ontologies/HSAPDV/11... | 52181d59df84578ed69214a5cb614036 | https://github.com/obophenotype/developmental-... | 2024-01-07 21:26:16.913885+00:00 | 2024-01-07 21:26:16.913894+00:00 | 1 |
| 49 | JIKv | DevelopmentalStage | mouse | True | mmusdv | Mouse Developmental Stages | 2020-03-10 | http://aber-owl.net/media/ontologies/MMUSDV/9/... | 5bef72395d853c7f65450e6c2a1fc653 | https://github.com/obophenotype/developmental-... | 2024-01-07 21:26:16.913985+00:00 | 2024-01-07 21:26:16.913994+00:00 | 1 |
| 50 | clid | Ethnicity | human | True | hancestro | Human Ancestry Ontology | 3.0 | https://github.com/EBISPOT/hancestro/raw/3.0/h... | 76dd9efda9c2abd4bc32fc57c0b755dd | https://github.com/EBISPOT/hancestro | 2024-01-07 21:26:16.914086+00:00 | 2024-01-07 21:26:16.914095+00:00 | 1 |
| 51 | rsbG | BioSample | all | True | ncbi | NCBI BioSample attributes | 2023-09 | s3://bionty-assets/df_all__ncbi__2023-09__BioS... | 918db9bd1734b97c596c67d9654a4126 | https://www.ncbi.nlm.nih.gov/biosample/docs/at... | 2024-01-07 21:26:16.914186+00:00 | 2024-01-07 21:26:16.914195+00:00 | 1 |
Show code cell content
!lamin delete --force test-developmental-stage
!rm -r test-developmental-stage
💡 deleting instance testuser1/test-developmental-stage
✅ deleted instance settings file: /home/runner/.lamin/instance--testuser1--test-developmental-stage.env
✅ instance cache deleted
✅ deleted '.lndb' sqlite file
❗ consider manually deleting your stored data: /home/runner/work/lamin-usecases/lamin-usecases/docs/test-developmental-stage