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Biosample analysis

Repo for analysis of biosamples in INSDC

Questions to explore

  • which attributes/properties are used
  • are these conformant to standards?
    • E.g. are MIxS fields used
    • Does the range constraint apply?
  • Can we mine ontology terms, e.g. ENVO from text descriptions
  • can we auto-populate metadata fields

Workflow

See Makefile for details

Analysis Data

In addition to the data in the target directory, sample data that is too large for GitHub is stored our Google drive here.
Files include:

  • biosample_set.xml.gz
    This is the full raw biosample dataset formatted as XML.

  • harmonized-values-eav.tsv.gz
    A tab-delimited file containing data extracted from biosample_set.xml.gz that contains the biosample's primary id and only the biosample attributes that have harmonized_name property. The data is in entity-attribute-value (EAV) format. The columns in the file are accession|attribute|value (accession is the accession number of the biosample).
    If necessary, use make target/harmonized-table.tsv to create the (non-zipped) file locally.

  • harmonized-table.tsv.gz
    A tab-delimited file in the data from harmonized-table.tsv.gz has been "pivoted" into a standard tabular format (i.e., the attributes are column headers). If necessary, use make harmonized-table.tsv to create the (non-zipped) file locally.

  • harmonized-attribute-value.ttl.gz
    A tab-delimited file in which the data from harmonized-values-eav.tsv.gz have been transformed into sets of turtle triples.
    If necessary, use make harmonized-attribute-value.ttl to create the (non-zipped) file locally.

  • harmonized-table.parquet.gz
    A parquet file containing the same contents as harmonized-table.tsv.gz. In pandas, you load like this: df = pds.read_parquet('harmonized-table.parquet.gz')
    You will need to have pyarrow installed (i.e., pip install pyarrow).
    If necessary, use make target/harmonized-table.parquet.gz to create the parquet file locally.
    Details of how to save the harmonized dataframe in parquet are found in save-harmonized-table-to-parquet.py.

  • harmonized_table.db.gz
    An sqlite database in which the biosample table contains the contents of harmonized-table.tsv.gz. Data is loaded into a pandas dataframe like this:

    con = sqlite3.connect('harmonized_table.db') # connect to database
df = pds.read_sql('select * from biosample limit 10', con) # test loading 10 records

    NB: Loading all records (i.e, df = pds.read_sql('select * from biosample', con)) is a VERY time consuming and memory intensive. I gave up after letting the process run for 4 hours. If necessary, use make target/harmonized_table.db to create the (non-zipped) sqlite database locally.
    Details of how to save the harmonized dataframe in sqlite are found in save-harmonized-table-to-sqlite.py

Related

https://github.com/cmungall/metadata_converter

https://academic.oup.com/database/article/doi/10.1093/database/bav126/2630130

Example bad data

Depth

MIxS specifies this should be {number} {unit}

Some example values that do not conform:

  • N40.1164_W88.2543
  • 25 santimeters
  • 0 – 20 cm
  • 3.149
  • 30-60cm replicate6
  • 1800, 1800
  • 30ft
  • 5m, 32m, 70m, 110m, 200m, 320m, 1000m
  • Surface soil from deep water
  • 0 m water depth
  • Metamorph4 (19dpf) biological replicate 3

pH

  • pH 7.9
  • 6.0-9.5
  • 8,156
  • NA1
  • 2.75 (orig)
  • 5.11±0.10
  • Missing: Not reported
  • Not collected
  • 7.0-7.5 um
  • Moderately alkaline

Note that missing values do not correspond to:

https://gensc.org/uncategorized/reporting-missing-values/

ammonium

Should be {float} {unit}

  • 0.71 micro molar
  • 14.941
  • -0.024
  • 1.9 g NH4-N L-1
  • Below the deteciton limit (2 microM)
  • 3.09µg/L

Units vary from 'micro molar' through uM through mg/L

geo_loc_name

MIxS:

The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ)

{term};{term};{text}

  • USA: WA
  • USA:MO
  • USA: Boston, MA
  • USA:CA:Davis
  • United Kingdom: Midlands and East of England
  • Malawi: GAZ