The BIOS project has generated for over 4000 individuals RNA-sequencing and DNA methylation data. A part from these data, GoNL imputed genotypes were generated from existing genotypes and several phenotypes/demographic variables were collected for the same set of samples. A highly flexible sample-oriented metadatabase (MDb) was created in order to manage the dynamic generation of this large-scale multiple-omic data set.

The MDb is a non-relation database (http://couchdb.apache.org/) that uses JSON to store records and JavaScript for querying. Furthermore, it has an HTTP API suitable to programmatically access the database from the GRID, e.g, the bios alignment pipeline.

Each record or document is a sample (individual) within the BIOS project and has a unique identifier.

Each document has a predefined structure according to our database schema. Custom R scripts are used to update or modify the database (see).

Access to the metadatabase (MDb) is restricted; please contact (Leon Mei).

Description of MDb content

The MDb contains as much as meta-information as possible from all samples and datatypes: location of (raw) data on srm, md5 checksum verification, quality control information, links between the different identifiers used (person_id, dna_id, etc) and phenotype information.

Every sample’s meta information is encoded in a CouchDB document. Each document has a unique identifier (the bios_id) which is biobankname (CODAM, LL, LLS, NTR, RS and PAN) concatenated with person_id separated by a “-”, e.g. CODAM-2001. This unique bios_id is not suitable for use in the public domain, e.g., EGA upload, therefore a unique non-identifiable identifier has been created for each individual; the uuid.

Every update of a sample in the database is recorded by increasing a revision number. Therefore it is always possible to undo wrong updates.

Description available views

Views are the way to extract information from the couchDb. Views are organized into designs; each design contains a number of views related to a particular kind of information that can be extracted from the MDb. For example, there is a design EGA which contains currently two views 1) freeze1RNASeq to extract those samples for which RNAseq data has been uploaded to EGA and 2) freeze1Methylation for the DNA methylation data.

Other relevant views are:

design: view:
Identifiers Ids, Relations
Phenotypes Phenotypes
RNA Fastq, RNARuns, RNASamplesheet
DNAm Idat, DNAmRuns, DNAmSamplesheet
DNA Imputations
EGA freeze1RNA, freeze1DNAm, freeze2RNA, freeze2DNAm

Note: We can always add views if necessary; please contact Leon Mei.

Accessing the MDb

Views can be downloaded as JSON documents by making a GET request. Most programming languages have utilities for making GET requests and to transform JSON documents. Some programming languages have an API for CouchDB e.g. JAVA and Python. There are several online tools available for transforming JSON documents to csv files.

head(getView("getIds", usrpwd=RP3_MDB_USRPWD, url=RP3_MDB))
## No username and password provided for the MDB use stored views!
##          ids    bios_id         uuid biobank_id person_id pheno_id gwas_id
## 1 CODAM-2037 CODAM-2037 BIOS71A89511      CODAM      2037     2037    2037
## 2 CODAM-2074 CODAM-2074 BIOS5BC078C7      CODAM      2074     2074    2074
## 3 CODAM-2175 CODAM-2175 BIOS78A709E9      CODAM      2175     2175    2175
## 4 CODAM-2555 CODAM-2555 BIOS700411C4      CODAM      2555     2555    2555
## 5   LLS-1114   LLS-1114 BIOS75EAD30E        LLS      1114     1114    1114
## 6    LLS-129    LLS-129 BIOSD87462DA        LLS       129      129     129
##   dna_id rna_id                rna_note gonl_id old_gonl_id cg_id in_rp3
## 1   2037   2037 library-prep: succeeded    <NA>        <NA>  <NA>  FALSE
## 2   2074   2074 library-prep: succeeded    <NA>        <NA>  <NA>  FALSE
## 3   2175   2175 library-prep: succeeded    <NA>        <NA>  <NA>  FALSE
## 4   2555   2555 library-prep: succeeded    <NA>        <NA>  <NA>  FALSE
## 5   1114   1114 library-prep: succeeded    <NA>        <NA>  <NA>  FALSE
## 6    129    129 library-prep: succeeded    <NA>        <NA>  <NA>  FALSE
head(getView("getFastq", usrpwd=RP3_MDB_USRPWD, url=RP3_MDB))
## No username and password provided for the MDB use stored views!
##              ids                                          run_id
## 1       LLS-2819                 BD1NYRACXX-5-27_AC1JL5ACXX-6-27
## 2        RS-3151 AC1JL5ACXX-8-25_BC52YAACXX-4-25_AC1K4KACXX-1-25
## 3     CODAM-2020                                  BD1NYRACXX-5-4
## 4     CODAM-2567                                  AD10W1ACXX-6-8
## 5 LL-LLDeep_0025                                  AD19YAACXX-3-3
## 6 LL-LLDeep_0057                                 AD19YAACXX-7-20
##   biobank_id
## 1        LLS
## 2         RS
## 3      CODAM
## 4      CODAM
## 5         LL
## 6         LL
##                                                                                                                                                                           R1
## 1                                 srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/RP3/RNASeq/BD1NYRACXX-5-27_AC1JL5ACXX-6-27/BD1NYRACXX-5-27_AC1JL5ACXX-6-27_R1.fq.gz
## 2 srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/RP3/RNASeq/AC1JL5ACXX-8-25_BC52YAACXX-4-25_AC1K4KACXX-1-25/AC1JL5ACXX-8-25_BC52YAACXX-4-25_AC1K4KACXX-1-25_R1.fq.gz
## 3                                                                   srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/RP3/RNASeq/BD1NYRACXX-5-4/BD1NYRACXX-5-4_R1.fq.gz
## 4                                                                   srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/RP3/RNASeq/AD10W1ACXX-6-8/AD10W1ACXX-6-8_R1.fq.gz
## 5                                                                   srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/RP3/RNASeq/AD19YAACXX-3-3/AD19YAACXX-3-3_R1.fq.gz
## 6                                                                 srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/RP3/RNASeq/AD19YAACXX-7-20/AD19YAACXX-7-20_R1.fq.gz
##                                                                                                                                                                           R2
## 1                                 srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/RP3/RNASeq/BD1NYRACXX-5-27_AC1JL5ACXX-6-27/BD1NYRACXX-5-27_AC1JL5ACXX-6-27_R2.fq.gz
## 2 srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/RP3/RNASeq/AC1JL5ACXX-8-25_BC52YAACXX-4-25_AC1K4KACXX-1-25/AC1JL5ACXX-8-25_BC52YAACXX-4-25_AC1K4KACXX-1-25_R2.fq.gz
## 3                                                                   srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/RP3/RNASeq/BD1NYRACXX-5-4/BD1NYRACXX-5-4_R2.fq.gz
## 4                                                                   srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/RP3/RNASeq/AD10W1ACXX-6-8/AD10W1ACXX-6-8_R2.fq.gz
## 5                                                                   srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/RP3/RNASeq/AD19YAACXX-3-3/AD19YAACXX-3-3_R2.fq.gz
## 6                                                                 srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/RP3/RNASeq/AD19YAACXX-7-20/AD19YAACXX-7-20_R2.fq.gz
head(getView("getIdat", usrpwd=RP3_MDB_USRPWD, url=RP3_MDB))
## No username and password provided for the MDB use stored views!
##                        ids            run_id biobank_id
## 1                 LLS-1311 8784233103_R04C01        LLS
## 2                 LLS-1865 8784233103_R04C02        LLS
## 3                 LLS-3085 8795207034_R01C01        LLS
## 4  NTR-A1016D-NTR00805-564 3999547094_R06C02        NTR
## 5 NTR-A1358C-NTR01757-1088 3999547104_R02C01        NTR
## 6  NTR-A643D-NTR01679-1041 3999547104_R01C01        NTR
##                                                                                                                             Grn
## 1 srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/RP3/IlluminaHumanMethylation450k/8784233103/8784233103_R04C01_Grn.idat
## 2 srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/RP3/IlluminaHumanMethylation450k/8784233103/8784233103_R04C02_Grn.idat
## 3 srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/RP3/IlluminaHumanMethylation450k/8795207034/8795207034_R01C01_Grn.idat
## 4 srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/RP3/IlluminaHumanMethylation450k/3999547094/3999547094_R06C02_Grn.idat
## 5 srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/RP3/IlluminaHumanMethylation450k/3999547104/3999547104_R02C01_Grn.idat
## 6 srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/RP3/IlluminaHumanMethylation450k/3999547104/3999547104_R01C01_Grn.idat
##                                                                                                                             Red
## 1 srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/RP3/IlluminaHumanMethylation450k/8784233103/8784233103_R04C01_Red.idat
## 2 srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/RP3/IlluminaHumanMethylation450k/8784233103/8784233103_R04C02_Red.idat
## 3 srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/RP3/IlluminaHumanMethylation450k/8795207034/8795207034_R01C01_Red.idat
## 4 srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/RP3/IlluminaHumanMethylation450k/3999547094/3999547094_R06C02_Red.idat
## 5 srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/RP3/IlluminaHumanMethylation450k/3999547104/3999547104_R02C01_Red.idat
## 6 srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/RP3/IlluminaHumanMethylation450k/3999547104/3999547104_R01C01_Red.idat
head(getView("getRNASeqRuns", usrpwd=RP3_MDB_USRPWD, url=RP3_MDB))
## No username and password provided for the MDB use stored views!
##          ids biobank_id rna_id          run_id     type freeze          qc
## 1 CODAM-2020      CODAM   2020  BD1NYRACXX-5-4 original   <NA>      passed
## 2 CODAM-2020      CODAM   2020  BD2D5MACXX-7-4    rerun   <NA>      passed
## 3 CODAM-2025      CODAM   2025  AC1JL5ACXX-5-5    rerun   <NA>      passed
## 4 CODAM-2027      CODAM   2027  AC1JL5ACXX-5-6    rerun   <NA>      passed
## 5 CODAM-2027      CODAM   2027  BC52YAACXX-3-6    rerun   <NA>      passed
## 6 CODAM-2041      CODAM   2041 AC1JL5ACXX-5-10    rerun   <NA> bad quality
##        raw past_filter
## 1 37467000    29654000
## 2 27211000    24023000
## 3 29218448    26728164
## 4 26712264    25050862
## 5 39473440    35320148
## 6     8516        7790
head(getView("getMethylationRuns", usrpwd=RP3_MDB_USRPWD, url=RP3_MDB))
## No username and password provided for the MDB use stored views!
##                        ids biobank_id dna_id            run_id      type
## 1                 LLS-1311        LLS   1311 8784233103_R04C01 replicate
## 2                 LLS-1865        LLS   1865 8784233103_R04C02 replicate
## 3                 LLS-3085        LLS   3085 8795207034_R01C01 replicate
## 4  NTR-A1016D-NTR00805-564        NTR    564 3999547094_R06C02 replicate
## 5 NTR-A1358C-NTR01757-1088        NTR   1088 3999547104_R02C01 replicate
## 6  NTR-A643D-NTR01679-1041        NTR   1041 3999547104_R01C01 replicate
##   freeze     qc
## 1   <NA> passed
## 2   <NA> passed
## 3   <NA> passed
## 4   <NA> passed
## 5   <NA> passed
## 6   <NA> passed
head(getView("getGenotypes", usrpwd=RP3_MDB_USRPWD, url=RP3_MDB))
## No username and password provided for the MDB use stored views!
##          ids biobank_id gonl_id gwas_id relation_type relation_id
## 1 CODAM-2001      CODAM    <NA>    2001          <NA>        <NA>
## 2 CODAM-2002      CODAM    <NA>    2002          <NA>        <NA>
## 3 CODAM-2009      CODAM    <NA>    2009          <NA>        <NA>
## 4 CODAM-2013      CODAM    <NA>    2013          <NA>        <NA>
## 5 CODAM-2016      CODAM    <NA>    2016          <NA>        <NA>
## 6 CODAM-2017      CODAM    <NA>    2017          <NA>        <NA>
##   imputation_reference1 imputation_id1 imputation_reference2
## 1                   HRC        73_2001                GoNLv5
## 2                   HRC        81_2002                GoNLv5
## 3                   HRC        66_2009                GoNLv5
## 4                   HRC        82_2013                GoNLv5
## 5                   HRC         1_2016                GoNLv5
## 6                   HRC       138_2017                GoNLv5
##   imputation_id2
## 1           2001
## 2           2002
## 3           2009
## 4           2013
## 5           2016
## 6           2017
head(getView("getImputations", usrpwd=RP3_MDB_USRPWD, url=RP3_MDB))
## No username and password provided for the MDB use stored views!
##          ids         uuid biobank_id gonl_id gwas_id imputation_reference
## 1 CODAM-2001 BIOS6DB3BAD1      CODAM    <NA>    2001               GoNLv5
## 2 CODAM-2001 BIOS6DB3BAD1      CODAM    <NA>    2001                  HRC
## 3 CODAM-2002 BIOSCFA14234      CODAM    <NA>    2002               GoNLv5
## 4 CODAM-2002 BIOSCFA14234      CODAM    <NA>    2002                  HRC
## 5 CODAM-2009 BIOSCA449668      CODAM    <NA>    2009               GoNLv5
## 6 CODAM-2009 BIOSCA449668      CODAM    <NA>    2009                  HRC
##   imputation_id
## 1          2001
## 2       73_2001
## 3          2002
## 4       81_2002
## 5          2009
## 6       66_2009
head(getView("getRelations", usrpwd=RP3_MDB_USRPWD, url=RP3_MDB))
## No username and password provided for the MDB use stored views!
##          ids         uuid biobank_id gonl_id gwas_id relation_type
## 1 CODAM-2001 BIOS6DB3BAD1      CODAM    <NA>    2001          <NA>
## 2 CODAM-2002 BIOSCFA14234      CODAM    <NA>    2002          <NA>
## 3 CODAM-2009 BIOSCA449668      CODAM    <NA>    2009          <NA>
## 4 CODAM-2013 BIOS415A8BFB      CODAM    <NA>    2013          <NA>
## 5 CODAM-2016 BIOSD16ED999      CODAM    <NA>    2016          <NA>
## 6 CODAM-2017 BIOSD2B838B2      CODAM    <NA>    2017          <NA>
##   relation_id
## 1        <NA>
## 2        <NA>
## 3        <NA>
## 4        <NA>
## 5        <NA>
## 6        <NA>
head(getView("allPhenotypes", usrpwd=RP3_MDB_USRPWD, url=RP3_MDB))
## No username and password provided for the MDB use stored views!
##                            ids RNA_A260280ratio Lipids_BloodSampling_Date
## 1                   CODAM-2074              2.1                2006-10-18
## 2     NTR-A1002C-NTR08919-5282               NA                2006-05-01
## 3     NTR-A1002D-NTR03923-2414               NA                2004-06-01
## 4 NTR-A1003C-NTR06631-06D06684               NA                2004-11-01
## 5   NTR-A1007C-NT0027342-10068               NA                2010-03-01
## 6 NTR-A1008C-NTR00267-06D07105               NA                2004-08-01
##   TotChol LDLchol GWAS_DataGeneration_Date Baso_Perc
## 1    7.70      NA                     2012        NA
## 2    4.60    2.25                     <NA>       0.0
## 3    4.83    2.66                     <NA>        NA
## 4    6.24    3.16                     <NA>       3.2
## 5    5.60    3.37                     <NA>       0.9
## 6    6.06    3.67                     <NA>       0.6
##   CellCount_BloodSampling_Date CHCM LipidMed RNA_Sampling_Date LUC
## 1                         <NA>   NA        0        2006-10-18  NA
## 2                   2006-05-01   NA        0        2006-05-01  NA
## 3                   2004-06-01   NA        0        2004-06-01  NA
## 4                   2004-11-01   NA        0        2004-11-01  NA
## 5                   2010-03-01   NA        0        2010-03-01  NA
## 6                   2004-08-01   NA        0        2004-08-01  NA
##   DNA_A260A280ratio  WBC DNA_Extraction_Method HDLchol RNA_Source
## 1              1.97   NA    QIAamp DNA minikit    1.85   PAX gene
## 2                NA 5.70                  <NA>    1.90   PAX gene
## 3                NA   NA                  <NA>    1.70   PAX gene
## 4                NA 5.90                  <NA>    0.72   PAX gene
## 5                NA 4.63                  <NA>    1.90   PAX gene
## 6                NA 5.20                  <NA>    1.99   PAX gene
##   DNA_QuantificationMethod               DNA_Source RNA_Extraction_Date
## 1                 nanodrop whole blood (buffy coat)          2010-07-01
## 2                     <NA>   Whole peripheral blood                <NA>
## 3                     <NA>   Whole peripheral blood                <NA>
## 4                     <NA>   Whole peripheral blood                <NA>
## 5                     <NA>   Whole peripheral blood                <NA>
## 6                     <NA>   Whole peripheral blood                <NA>
##   Granulocyte_Perc CellCount_BloodSampling_Time CRP_BloodSampling_Time
## 1               NA                         <NA>                   <NA>
## 2             60.5                         7:45                   7:45
## 3               NA                         9:25                   9:25
## 4             55.3                         8:00                   8:00
## 5             60.1                         9:30                   9:30
## 6             59.9                         9:40                   9:40
##   RNA_Sampling_Time  RBC LUC_Perc DNA_BloodSampling_Age
## 1          00:00:00   NA       NA                  69.3
## 2          07:45:00 4.49       NA                  25.6
## 3          09:25:00   NA       NA                  24.7
## 4          08:00:00 5.19       NA                  25.5
## 5          09:30:00 4.21       NA                  43.9
## 6          09:40:00 4.48       NA                  41.3
##   Lipids_BloodSampling_Age hsCRP Neut Smoking DNA_BloodSampling_Date
## 1                     69.3  0.50   NA       0             2006-10-18
## 2                     25.6  1.50 3.40       0             2006-05-01
## 3                     24.7  7.20   NA       2             2004-06-01
## 4                     25.5  1.40 2.90       0             2004-11-01
## 5                     43.9  0.28 2.63       0             2010-03-01
## 6                     41.3  0.36 2.90       2             2004-08-01
##   RNA_BloodSampling_Age  RDW CH  HCT DNA_Extraction_Date Mono Lymph
## 1                  69.3   NA NA   NA          2012-05-01   NA    NA
## 2                  25.6 11.0 NA 0.43                <NA>  0.3  1.90
## 3                  24.7   NA NA   NA                <NA>   NA    NA
## 4                  25.5 11.9 NA 0.46                <NA>  0.5  2.10
## 5                  43.9 12.6 NA 0.38                <NA>  0.4  1.45
## 6                  41.3 12.1 NA 0.41                <NA>  0.4  1.70
##   CRP_BloodSampling_Date Granulocyte LipidsMed_Age RNA_RIN BirthYear
## 1             2006-10-18          NA            NA     8.7      1937
## 2             2006-05-01        3.50          25.6      NA      1980
## 3             2004-06-01          NA          24.7      NA      1980
## 4             2004-11-01        3.30          25.5      NA      1980
## 5             2010-03-01        2.78          43.9      NA      1966
## 6             2004-08-01        3.10          41.3      NA      1962
##   Lymph_Perc             RNA_Extraction_Method Mono_Perc
## 1         NA PAXgene blood miRNA kit (Qiacube)        NA
## 2       33.6                              <NA>       5.9
## 3         NA                              <NA>        NA
## 4       36.4                              <NA>       8.3
## 5       31.3                              <NA>       8.6
## 6       32.7                              <NA>       7.4
##                     GWAS_Chip Baso Eos_Perc HGB Neut_Perc  Eos
## 1 Illumina human omni express   NA       NA  NA        NA   NA
## 2                        <NA> 0.00      1.8 9.1      58.7 0.10
## 3                        <NA>   NA       NA  NA        NA   NA
## 4                        <NA> 0.20      3.5 9.9      48.6 0.20
## 5                        <NA> 0.04      2.4 7.8      56.8 0.11
## 6                        <NA> 0.00      3.9 8.5      55.4 0.20
##   CRP_BloodSampling_Age PLT Weight HDW Anthropometry_Age LDLcholMethod
## 1                  69.3  NA  74.75  NA              69.3            NA
## 2                  25.6 244  58.00  NA              25.6             1
## 3                  24.7  NA  52.00  NA              24.7             1
## 4                  25.5 222  78.00  NA              25.5             1
## 5                  43.9 249  88.00  NA              43.9             1
## 6                  41.3 250  65.00  NA              41.3             1
##    MCHC Sex  MPV                             Ascertainment_criterion
## 1    NA   1   NA Selected for mildly increased DM2 /CVD risk factors
## 2 21.10   1  9.1                                                <NA>
## 3    NA   1   NA                                                <NA>
## 4 21.50   0  8.3                                                <NA>
## 5 20.80   1 11.5                                                <NA>
## 6 20.85   1  8.8                                                <NA>
##   CellCount_BloodSampling_Age Smoking_Age Lipids_BloodSampling_Time  MCH
## 1                          NA        69.3                   8-11 am   NA
## 2                        25.6        25.6                      7:45 2.03
## 3                        24.7        24.7                      9:25   NA
## 4                        25.5        25.5                      8:00 1.91
## 5                        43.9        43.9                      9:30   NA
## 6                        41.3        41.3                      9:40 1.90
##    MCV Height Triglycerides Lipids_BloodSampling_Fasting
## 1   NA  165.3          1.30                            1
## 2 96.0  164.0          0.99                            1
## 3   NA  168.0          1.02                            1
## 4 88.8  179.0          5.13                            1
## 5 89.1  176.0          0.73                            1
## 6 91.1  173.0          0.88                            1
##   DNA_BloodSampling_Time
## 1               00:00:00
## 2               07:45:00
## 3               09:25:00
## 4               08:00:00
## 5               09:30:00
## 6               09:40:00
head(getView("rnaseqSamplesheet", usrpwd=RP3_MDB_USRPWD, url=RP3_MDB))
## No username and password provided for the MDB use stored views!
##              ids                                          run_id run_num
## 1        RS-3151 AC1JL5ACXX-8-25_BC52YAACXX-4-25_AC1K4KACXX-1-25    <NA>
## 2     CODAM-2020                                  BD1NYRACXX-5-4     125
## 3     CODAM-2567                                  AD10W1ACXX-6-8     234
## 4 LL-LLDeep_0025                                  AD19YAACXX-3-3     164
## 5 LL-LLDeep_0057                                 AD19YAACXX-7-20     164
## 6 LL-LLDeep_0077                                 AC1C40ACXX-8-18     142
##   flowcell_num machine       raw past_filter       date insert_size
## 1         <NA>    <NA> 115866354   101558658       <NA>          NA
## 2           2b  SN1013  37467000    29654000 2013-03-29    321.0000
## 3           3a   SN505  33216000    29569000 2013-04-17    309.0000
## 4          15b  SN1013  28427642    23488692 2013-09-27    321.2560
## 5          15b  SN1013  32253158    28344848 2013-09-27    314.9758
## 6           5b  SN1013  36156000    29822000 2013-05-16    313.0000
head(getView("methylationSamplesheet", usrpwd=RP3_MDB_USRPWD, url=RP3_MDB))
## No username and password provided for the MDB use stored views!
##                        ids         uuid biobank_id            run_id
## 1                 LLS-1311 BIOSDB2BAFE0        LLS 8784233103_R04C01
## 2                 LLS-1865 BIOS92B3DB30        LLS 8784233103_R04C02
## 3                 LLS-3085 BIOSE66BBFF7        LLS 8795207034_R01C01
## 4  NTR-A1016D-NTR00805-564 BIOS29AAC0A3        NTR 3999547094_R06C02
## 5 NTR-A1358C-NTR01757-1088 BIOSB2AFC925        NTR 3999547104_R02C01
## 6  NTR-A643D-NTR01679-1041 BIOSF8305A84        NTR 3999547104_R01C01
##   C2_Lotnumber Sentrix_Lotnumber  Scan_Date   TEM_Barcode Sentrix_Barcode
## 1      8783644           8784233 2013-06-25 wg0592288-tem      8784233103
## 2      8783644           8784233 2013-06-25 wg0592288-tem      8784233103
## 3      8783644           8795207 2013-06-25 wg0595416-tem      8795207034
## 4      9701991           3999547 2015-02-02 wg2530283-tem      3999547094
## 5      9701991           3999547 2015-02-02 wg2530283-tem      3999547104
## 6      9701991           3999547 2015-02-02 wg2530283-tem      3999547104
##      C1_Barcode Scan_Time Stain_Date Sentrix_Position    C2_Barcode
## 1 wg0516321-xc1  16:10:04 2013-06-25           R04C01 wg0526054-xc2
## 2 wg0516321-xc1  16:25:25 2013-06-25           R04C02 wg0526054-xc2
## 3 wg0514750-xc1  18:57:16 2013-06-25           R01C01 wg0525416-xc2
## 4 wg2509473-xc1  09:54:33 2015-01-30           R06C02 wg2508257-xc2
## 5 wg2509473-xc1  10:01:39 2015-01-30           R02C01 wg2508257-xc2
## 6 wg2509473-xc1  09:59:34 2015-01-30           R01C01 wg2508257-xc2
##   ATM_Lotnumber TEM_Lotnumber Library_Date Sample_Well   ATM_Barcode
## 1       8762691       8615771   2013-06-18         H08 wg0535787-atm
## 2       8762691       8615771   2013-06-18         F09 wg0535787-atm
## 3       8762691       8615771   2013-06-18         A10 wg0535590-atm
## 4       9807148       9701993   2015-01-28         D02 wg2585412-atm
## 5       9807148       9701993   2015-01-28         F02 wg2585412-atm
## 6       9807148       9701993   2015-01-28         E02 wg2585412-atm
##   Hybridization_Date   STM_Barcode C1_Lotnumber Scanner_Name Sample_Plate
## 1         2013-06-24 wg1577023-stm      8784516         N140            6
## 2         2013-06-24 wg1577023-stm      8784516         N140            6
## 3         2013-06-24 wg1576143-stm      8784516         N140            8
## 4         2015-01-29 wg1651808-stm      9701989         N140 OV0192DNA002
## 5         2015-01-29 wg1651808-stm      9701989         N140 OV0192DNA002
## 6         2015-01-29 wg1651808-stm      9701989         N140 OV0192DNA002
##   STM_Lotnumber
## 1       9284859
## 2       9284859
## 3       9284859
## 4       9701999
## 5       9701999
## 6       9701999

Access the metadatabase using R

BBMRIomics uses a configuration file to read in your MDb username and password, so that you do not have to type it every time you use the MDb.

Create a file called .bbmriomics (.biosrutils is also a valid name) and stored it in your home directory on the VM (/home/username) and add e.g.:

usrpwdrp3: 'rp3_username:password' 
usrpwdrp4: 'rp4_username:password'
proxy:  /tmp/your_proxy

The first line contains your username and password for the RP3 database. The latter two can be optionally for accessing the RP4 database and accessing data from SRM using the function SRM2VM.

On loading the BBMRIomics library your username and password will be set in the variable RP3_MDB_USRPWD. The getView-function can now be used like this:

ids <- getView("getIds", usrpwd=RP3_MDB_USRPWD, url=RP3_MDB)
## No username and password provided for the MDB use stored views!

Also, access to the RNAseq run database (if you requested an account) is possible through the getView-function.

stats <- getView("getStats", usrpwd=RP3_MDB_USRPWD, url=RP3_RDB)
## No username and password provided for the MDB use stored views!