Ensembl species -> bionty.Species().df

Downloaded from: https://www.ensembl.org/info/about/species.html

import lamindb as ln
import pandas as pd
from lnschema_bionty import id

ln.nb.header()

2022-10-24 16:54:15,372:INFO - Note: NumExpr detected 10 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8.
2022-10-24 16:54:15,373:INFO - NumExpr defaulting to 8 threads.

author	Sunny Sun (sunnyosun)
id	SH5O08MYHNXe
version	1
time_init	2022-10-24 10:21
time_run	2022-10-24 14:55
consecutive_cells	True
pypackage	lamindb==0.6.0 lnschema_bionty==0.4.3 pandas==1.5.0

Curate the species table

df = pd.read_csv("https://bionty-assets.s3.amazonaws.com/Species.csv", dtype=str)

df.head()

	Common name	Scientific name	Taxon ID	Ensembl Assembly	Accession	Genebuild Method	Variation database	Regulation database
0	Abingdon island giant tortoise	Chelonoidis abingdonii	106734	ASM359739v1	GCA_003597395.1	Full genebuild	-	-
1	African ostrich	Struthio camelus australis	441894	ASM69896v1	GCA_000698965.1	Full genebuild	-	-
2	Agassiz's desert tortoise	Gopherus agassizii	38772	ASM289641v1	GCA_002896415.1	Full genebuild	-	-
3	Algerian mouse	Mus spretus	10096	SPRET_EiJ_v1	GCA_001624865.1	External annotation import	-	Y
4	Alpaca	Vicugna pacos	30538	vicPac1	-	Projection build	-	-

df = df[
    ["Common name", "Taxon ID", "Scientific name", "Ensembl Assembly", "Accession"]
].copy()

df.head()

	Common name	Taxon ID	Scientific name	Ensembl Assembly	Accession
0	Abingdon island giant tortoise	106734	Chelonoidis abingdonii	ASM359739v1	GCA_003597395.1
1	African ostrich	441894	Struthio camelus australis	ASM69896v1	GCA_000698965.1
2	Agassiz's desert tortoise	38772	Gopherus agassizii	ASM289641v1	GCA_002896415.1
3	Algerian mouse	10096	Mus spretus	SPRET_EiJ_v1	GCA_001624865.1
4	Alpaca	30538	Vicugna pacos	vicPac1	-

Generate bionty species ids

ids = []
for i in df.index:
    ids.append(id.species())

# make sure the ids are unique
assert df.index.is_unique

df.index = ids
df.index.name = "id"

df.head()

	Common name	Taxon ID	Scientific name	Ensembl Assembly	Accession
id
MfC	Abingdon island giant tortoise	106734	Chelonoidis abingdonii	ASM359739v1	GCA_003597395.1
oQH	African ostrich	441894	Struthio camelus australis	ASM69896v1	GCA_000698965.1
G2P	Agassiz's desert tortoise	38772	Gopherus agassizii	ASM289641v1	GCA_002896415.1
OC9	Algerian mouse	10096	Mus spretus	SPRET_EiJ_v1	GCA_001624865.1
Tns	Alpaca	30538	Vicugna pacos	vicPac1	-

df.to_parquet("ensembl_species.parquet")

Push to bionty-assets.lndb

!lndb load bionty-assets

migrate-unnecessary

!lndb login sunnyosun

ingest = ln.db.Ingest()

ingest.add("ensembl_species.parquet", dobject_id="VpdUdouFahpvStwddqTwk");

ingest.commit()

✅ Cell numbers increase consecutively: Awesome!

2022-10-24 16:54:51,715:INFO - Found credentials in shared credentials file: ~/.aws/credentials

Upload /Users/sunnysun/Documents/repos.nosync/bionty-assets/docs/ingest/ensembl_species.parquet: 1.00
ℹ️ Added notebook 'Ensembl species -> `bionty.Species().df`' (SH5O08MYHNXe, 1) by user sunnyosun.
✅ Ingested the following dobjects:
+---+-------------------------------------------------+--------------------------------------------------------------+----------------------+
|   | dobject                                         | jupynb                                                       | user                 |
+---+-------------------------------------------------+--------------------------------------------------------------+----------------------+
| 0 | ensembl_species.parquet (VpdUdouFahpvStwddqTwk) | 'Ensembl species -> `bionty.Species().df`' (SH5O08MYHNXe, 1) | sunnyosun (kmvZDIX9) |
+---+-------------------------------------------------+--------------------------------------------------------------+----------------------+
ℹ️ Set notebook version to 1 & wrote pypackages.

Now on S3: https://bionty-assets.s3.amazonaws.com/VpdUdouFahpvStwddqTwk.parquet