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ISA-tools / ISAvalidator-ISAconverter-BIImanager

The ISAvalidator, ISA converter and BII data manager tools
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Bii Manager does not import samples into DB. #54

Closed JustGitting closed 10 years ago

JustGitting commented 10 years ago

Hi,

Product: Bii Manager Version: 1.6.5

Platform: Red Hat Enterprise Linux Server release 5.5 (Tikanga) 64-bit Intel platform psql (PostgreSQL) 8.4.13

Severity: Normal

Summary: Bii Manager v1.6.5 does not load any sample records into the database if the records are not used in any assays.

Description:

I've set up Bii manager and Bii web app to use a postgres DB, which works fine. However, I've found that only records from assays are making it into the DB, whilst samples are not being loading into the DB if not used by any assays.

Steps to Reproduce:

  1. Open Bii Manager 1.6.5 (or any previous version)
  2. Load default configuration file (isaconfig-default_v2011-02-18)
  3. Select Upload icon.
  4. Select a ISA-tab that contains studies, but does not have all samples from the studies used in assays.
  5. Upload ISA-tab to database.
  6. Set permissions for curator.
  7. Success message is displayed.

Actual Results: Bii Manager reports that the upload is successful, but the postgres database does not contain any sample records.

Expected Results: Sample records uploaded and stored in the database.

Additional Information:

I initially imported the example ISA-tab BII-I-1 into a clean postgres database using BII manager with the following message after successfully uploading:

Investigation: BII-I-1 (Growth control of the eukaryote cell: a systems biology study in yeast)
Study: BII-S-2 (A time course analysis of transcription response in yeast treated with rapamycin, a specific inhibitor of the TORC1 complex: impact on yeast growth)
        Sample file: s_BII-S-2.txt with 14 samples
                Assay File: a_microarray.txt with 14 assays
                measurement transcription profiling
                technology DNA microarray
                platform Affymetrix

Study: BII-S-1 (Study of the impact of changes in flux on the transcriptome, proteome, endometabolome and exometabolome of the yeast Saccharomyces
cerevisiae under different nutrient limitations)
        Sample file: s_BII-S-1.txt with 162 samples
                Assay File: a_metabolome.txt with 111 assays
                measurement metabolite profiling
                technology mass spectrometry
                platform LC-MS/MS

                Assay File: a_proteome.txt with 3 assays
                measurement protein expression profiling
                technology mass spectrometry
                platform iTRAQ

                Assay File: a_transcriptome.txt with 48 assays
                measurement transcription profiling
                technology DNA microarray
                platform Affymetrix

Checking what is in the database is easy by dumping the database to a file and grepping.

 $ sudo pg_dump -C -U postgres bioinvindex > ./psql_dump_bioninvindex_withassays.sql
 $ grep culture1 ./psql_dump_bioninvindex_withassays.sql

which finds the following records:

32835   2014-02-05 12:56:57.256 BII-S-1:source:culture16        culture16       32852   98332
32854   2014-02-05 12:56:57.256 BII-S-1:source:culture11        culture11       32884   98332
32933   2014-02-05 12:56:57.256 BII-S-1:source:culture1 culture1        32985   98332
33044   2014-02-05 12:56:57.256 BII-S-1:source:culture10        culture10       33126   98332
33066   2014-02-05 12:56:57.256 BII-S-1:source:culture12        culture12       33153   98332
33282   2014-02-05 12:56:57.256 BII-S-1:source:culture17        culture17       33438   98332
33298   2014-02-05 12:56:57.256 BII-S-1:source:culture13        culture13       33459   98332
33323   2014-02-05 12:56:57.256 BII-S-1:source:culture14        culture14       33494   98332
33341   2014-02-05 12:56:57.256 BII-S-1:source:culture18        culture18       33519   98332

I then opened the BII-I-1 ISA-tab in ISA-Creator (v1.7.5) and deleted all assays from both studies and saved it as Example1_noassays_20140205. Using BII manager (v1.6.5) I removed the BII-I-1 and BII-I-2 from the DB so it was empty. Then uploaded the modified BII-I-1 ISA-tab (Example1_noassays_20140205) to the database using BII manager, and this time the message after successfully uploading the ISAtab was:

Investigation: BII-I-1-noassays (Growth control of the eukaryote cell: a systems biology study in yeast)
        Study: BII-S-2 (A time course analysis of transcription response in yeast treated with rapamycin, a specific inhibitor of the TORC1 complex: impact on yeast growth)
                Sample file: s_BII-S-2.txt with 0 samples

         Study: BII-S-1 (Study of the impact of changes in flux on the transcriptome, proteome, endometabolome and exometabolome of the yeast Saccharomyces cerevisiae under different nutrient limitations)
                Sample file: s_BII-S-1.txt with 0 samples

Even though BII manager reports "0 Samples", both study files contain records as shown below:

$ head -3 ./Example1_no_assays_20140205/s_BII-S-1.txt

"Source Name"   "Characteristics[organism]"     "Term Source REF"       "Term Accession Number" "Characteristics[strain]"       "Term Source REF"       "Term Accession Number" "Characteristics[genotype]"  "Term Source REF"       "Term Accession Number" "Protocol REF"  "Sample Name"   "Factor Value[limiting nutrient]"       "Term Source REF"       "Term Accession Number" "Factor Value[rate]" "Unit"  "Term Source REF"       "Term Accession Number"
"culture1"      "Saccharomyces cerevisiae"      "NCBITAXON"     "http://purl.obolibrary.org/obo/NCBITaxon_4932" "FY1679"        ""      ""      "KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD"   ""      ""      ""      "C-0.07-aliquot1"       "elemental carbon"      "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415"    "0.07"  "l/hour"    ""       ""
"culture1"      "Saccharomyces cerevisiae"      "NCBITAXON"     "http://purl.obolibrary.org/obo/NCBITaxon_4932" "FY1679"        ""      ""      "KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD"   ""      ""      ""      "C-0.07-aliquot2"       "elemental carbon"      "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33415"    "0.07"  "l/hour"    ""       ""

and 

$ head -3  ./Example1_no_assays_20140205/s_BII-S-2.txt
"Source Name"   "Characteristics[organism]"     "Term Source REF"       "Term Accession Number" "Characteristics[strain]"       "Term Source REF"       "Term Accession Number" "Characteristics[genotype]"  "Term Source REF"       "Term Accession Number" "Characteristics[mating type]"  "Term Source REF"       "Term Accession Number" "Protocol REF"  "Sample Name"   "Factor Value[dose]" "Unit"  "Term Source REF"       "Term Accession Number" "Factor Value[exposure time]"   "Unit"  "Term Source REF"       "Term Accession Number" "Factor Value[compound]"        "Term Source REF"    "Term Accession Number"
"NZ_0hrs_Grow_1"        "Saccharomyces cerevisiae"      "NCBITAXON"     "http://purl.obolibrary.org/obo/NCBITaxon_4932" "FY1679"        ""      ""      "KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD"   ""      ""      "alpha mating type (yeast)"     "OBI"   "http://purl.obolibrary.org/obo/PATO_0001344"   ""      "NZ_0hrs_Grow1_Sample_1"    "0"      "nanogram per milliliter"       "UO"    "http://purl.obolibrary.org/obo/UO_0000275"     "0"     "hour"  "UO"    "http://purl.obolibrary.org/obo/UO_0000032"     ""      ""      ""
"NZ_0hrs_Grow_1"        "Saccharomyces cerevisiae"      "NCBITAXON"     "http://purl.obolibrary.org/obo/NCBITaxon_4932" "FY1679"        ""      ""      "KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD"   ""      ""      "alpha mating type (yeast)"     "OBI"   "http://purl.obolibrary.org/obo/PATO_0001344"   ""      "NZ_1hrs_Grow1_Drug_Sample_1"
        "200"   "nanogram per milliliter"       "UO"    "http://purl.obolibrary.org/obo/UO_0000275"     "1"     "hour"  "UO"    "http://purl.obolibrary.org/obo/UO_0000032"     "sirolimus" "CHEBI"  "http://purl.obolibrary.org/obo/CHEBI_9168"

Again, dumping the database to file and searching for a sample name shows that the sample is not in the database.

$ sudo pg_dump -C -U postgres bioinvindex > ./psql_dump_bioninvindex_noassays.sql
$ grep culture1 ./psql_dump_bioninvindex_noassays.sql

In this case "culture1" is not found in the database dump.

Thanks for your help, please let me know if you need anything else.

Cheers

eamonnmag commented 10 years ago

Thanks for your message. For us, this is not an issue.

The BII is based around the concept of assayresults. If a sample is not used, we do not import it.

JustGitting commented 10 years ago

Hi Eamonn,

Thanks for the clarification.