2023-05-05
This is PMA's DBGI daily open-notebook.
Today is 2023.05.05
Todo today
Have a look at the DBGI discussion forum
- https://github.com/orgs/digital-botanical-gardens-initiative/discussions
Doing
Micro hackaton
Ana, Tarcisio, PM
- Prepare a subgraph for Tobias
- Make sure to add Ana to EMI mailing.
Sources of input data ? Who are the producers ?
- inat user collectors
- ms results
others ?
Where does this data go ?
- openBis
- wikibase
- KG
- directus.dbgi.com
- massive
Dataset DBGI"tropical" datset 135 or so plants coming from a tropical greenhouse in JBUF
https://www.degruyter.com/document/doi/10.1515/pac-2021-2007/html
Should be integer enpkg:has_row_id 6.0 ;
Think about the hard encoding of the dbgi ids in the Massive URL Benchmark this when we run the dbgi tropical set with the correct dbgi ids
enpkg:AAJKTJJGBYWRHK enpkg:has_npc_class enpkg:npc_Acetogenins ; enpkg:has_npc_pathway enpkg:npc_Polyketides ; enpkg:has_npc_superclass enpkg:npc_Linear_polyketides ; enpkg:has_smiles "CCCCCCCCCCCCC(C1CCC(O1)C2CCC(O2)CC(CCCCCC(CC3=CC(OC3=O)C)O)O)O" ; enpkg:is_InChIkey2D_of enpkg:AAJKTJJGBYWRHK-GJCPBGCDSA-N, enpkg:AAJKTJJGBYWRHK-QCOIHMLWSA-N, enpkg:AAJKTJJGBYWRHK-SCPMWOMPSA-N, enpkg:AAJKTJJGBYWRHK-UHFFFAOYSA-N .
Declare inchikey for example :
enpkg:AAJKTJJGBYWRHK enpkg:has_npc_class enpkg:npc_Acetogenins ; enpkg:has_InChIKey "AAJKTJJGBYWRHK" ; enpkg:has_npc_pathway enpkg:npc_Polyketides ; enpkg:has_npc_superclass enpkg:npc_Linear_polyketides ; enpkg:has_smiles "CCCCCCCCCCCCC(C1CCC(O1)C2CCC(O2)CC(CCCCCC(CC3=CC(OC3=O)C)O)O)O" ; enpkg:is_InChIkey2D_of enpkg:AAJKTJJGBYWRHK-GJCPBGCDSA-N, enpkg:AAJKTJJGBYWRHK-QCOIHMLWSA-N, enpkg:AAJKTJJGBYWRHK-SCPMWOMPSA-N, enpkg:AAJKTJJGBYWRHK-UHFFFAOYSA-N .
Tasks
PM:
- establish a graphical overview of this dataflow draw.io https://app.diagrams.net/#G1tmt-gJGJyj1DSSI1JhGonQqF1BCk-VY4
https://idsm.elixir-czech.cz/chemweb/ https://chembl.gitbook.io/chembl-interface-documentation/downloads https://pubchem.ncbi.nlm.nih.gov/docs/rdf
Huernia schneideriana
observation
dbgi_001057 ~ 155584652 dbgi_001057_01 dbgi_001057_01_01 20230505Z1400001_dbgi_001057_01.mzML
Discused with Audrey just now
Huernia schneideriana
observation
dbgi_001057 ~ 155584652 dbgi_001057_01 ~ extraction dbgi_001057_01_01 ~ vial dbgi_001057_01_02 ~ vial dbgi_001057_01_03 ~ vial dbgi_001057_01_04 ~ vial
20230505Z1400001_ALC_dbgi_001057_01_01.mzML 20230505Z1401101_ALC_dbgi_001057_01_01.mzML
species
Huernia schneideriana
observation
dbgi_001057 ~ 155584652 ~ CETAF
extract
dbgi_001057_01
mass spec run
dbgi_001057_01_02
mass spec filename
202305_Tarcisio_INternalSIB_01.mzML ~ MSV000090090 ~ DOI
species
Huernia schneideriana
observation
dbgi_001057 ~ 155584652 ~ CETAF0000001
extract
CETAF0000001_dbgi_001057_01
mass spec run
CETAF0000001_run
mass spec filename
202305_Tarcisio_INternalSIB_01.mzML ~ MSV000090090 ~ DOI
species
Huernia schneideriana
observation
dbgi_001057 ~ 155584652 ~ CETAF0000001
extract
CETAF0000001_PMA01
mass spec run
CETAF0000001_01_01
mass spec filename
202305_Tarcisio_INternalSIB_01.mzML ~ MSV000090091 ~ DOI
species
Huernia schneideriana
observation
dbgi_001057 ~ 155584652 ~ CETAF0000002
extract
CETAF0000002_PMA01
mass spec run
CETAF0000001_01_01
mass spec filename
202305_Tarcisio_INternalSIB_01.mzML ~ MSV000090091 ~ DOI
species
Huernia fliosososo
observation
TArciusooID01 ~ 1555841
extract
TArciusooID01_01
mass spec run
TArciusooID01_01_01
mass spec filename
202305_Tarcisio_INternalSIB_01.mzML
species
Huernia fliosososo
observation
TArciusooID01 ~ 1555841
extract
TArciusooID01_01
mass spec run
TArciusooID01_01_01
mass spec filename
202305_Tarcisio_INternalSIB_01.mzML
Huernia schneideriana dbgi_001057 ~ 155584652 dbgi_001057_02 dbgi_001057_02_01 20230505Z1400001_dbgi_001057_02.mzML
Huernia schneideriana dbgi_001088 ~ 1555878787 dbgi_001088_01 20240505Z1400001_dbgi_001088.mzML
Alpinia officinarum
DBGI_01_04_004 () DBGI_01_04_004_extract 20220513_PMA_DBGI_01_04_004.mzML
DBGI_01_04_004 () DBGI_01_04_004_extract 20220513_PMA_DBGI_01_04_004.mzML
Should be a requirement ? https://cetaf.org/resources/best-practices/#:~:text=CETAF%20Stable%20Identifiers&text=Stable%20identifiers%20are%20globally%20unique,them%20with%20the%20semantic%20web.
Lets discuss this with DONat https://riojournal.com/article/97374/
sample_filename_pos sample_id sample_type organism_species ipen sample_prep_mode sample_substance_name massive_id 20220513_PMA_DBGI_01_04_004.mzML DBGI_01_04_004 sample Alpinia officinarum XX 0 FRIBG 20040092 liquid_nitrogen DBGI_01_04_004_extract MSV000090090