INCATools biosample-analysis issues

INCATools / biosample-analysis

analysis of biosamples in INSDC

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issues

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Normalize unit representations

#32 wdduncan opened 4 years ago
0
run NER/CR over all textual metadata fields

#31 cmungall opened 4 years ago
1
Expand TSV to include closures of ontology classes (primarily EnvO)

#30 cmungall opened 4 years ago
0
removing top level notebooks dir

#29 realmarcin closed 4 years ago
0
Perform NER on sample metadata

#28 wdduncan closed 3 years ago
2
raw tsv to numeric notebook

#27 realmarcin closed 4 years ago
0
normalize missing values

#26 cmungall opened 4 years ago
2
normalize ENVO terms

#25 cmungall opened 4 years ago
11
normalize package names

#24 cmungall opened 4 years ago
4
add notebook profiling water package samples

#23 wdduncan closed 4 years ago
0
add non-human samples

#22 wdduncan closed 4 years ago
0
add scripts for creating sqlite and parquet files

#21 wdduncan closed 4 years ago
0
explore TPOT package for more automated transform, feature and model selection

#20 realmarcin opened 4 years ago
0
Subset columns to MIxS terms (version 5)

#19 wdduncan closed 3 years ago
4
change accession column to id; add BIOSAMPLE prefix to ids; change db_id colum to xref; Fixes #13

#18 wdduncan closed 4 years ago
0
identify key set of quantitative fields to predict environment terms

#17 realmarcin opened 4 years ago
0
first parquet analysis nb

#16 realmarcin closed 4 years ago
0
docs

#15 cmungall closed 4 years ago
0
pandas describe() output from parquet file

#14 realmarcin closed 4 years ago
2
Change accession attribute to ncbi:id

#13 wdduncan closed 4 years ago
0
update readme

#12 wdduncan closed 4 years ago
0
update readme

#11 wdduncan closed 4 years ago
0
update readme

#10 wdduncan closed 4 years ago
0
update readme with info about sqlite and parquet files

#9 wdduncan closed 4 years ago
0
Validate harmonized attributes using MIxS patterns

#8 cmungall opened 4 years ago
0
Additional fields to include

#7 cmungall closed 4 years ago
2
Only collect harmonized_name when building sample TSV

#6 cmungall closed 4 years ago
4
Translate to KGX edges format and use embiggen to embed and perform link prediction

#5 cmungall opened 4 years ago
0
Export canonical TSV for NMDC Sample data

#4 realmarcin closed 4 years ago
2
Are all fields at the Study level inherited by Samples?

#3 realmarcin opened 4 years ago
0
adding Magnify metadata download

#2 realmarcin closed 4 years ago
0
fetch study metadata

#1 cmungall opened 4 years ago
6