Extracted Terms list

mzML

Data Transformation Name
- type:
  list of cv terms
- definition:
  The successive transformation process the MS data underwent
  (all being subclasses of NMR:1400042)
- example value:
  {"entry_list": [
     {"accession": "http://purl.obolibrary.org/obo/MS_1000544",
      "name": "Conversion to mzML","ref": "MS"},
     {"accession": "http://purl.obolibrary.org/obo/MS_1000035",
      "name": "peak picking","ref": "MS"}
  ]}
Data Transformation software
- type:
  cv term
- definition:
  The software that was used for the data transformations
- example value:
  {"accession": "http://purl.obolibrary.org/obo/MS_1000615",
   "name": "ProteoWizard software","ref": "MS"}
Data Transformation software version
- type:
  free text
- definition
  The version of the data transformation software
- example value:
  {"value": "3.0.6002"}
Data file checksum type
- type
  cv term w/ value
- definition
  The type of the checksum used to check the data file integrity
- example value
  {"accession": "http://purl.obolibrary.org/obo/MS_1000569",
   "name": "SHA-1","ref": "MS",
   "value": "58f67219180d0e67da2b8f1652681b925371fcb9"}
Data file content
- type
  list of cv terms
- definition
  The contents of the Raw Data files
- example value
  {"entry_list": [
     {"accession": "http://purl.obolibrary.org/obo/MS_1000579",
      "name": "MS1 spectrum","ref": "MS"},
     {"accession": "http://purl.obolibrary.org/obo/MS_1000580",
      "name": "MSn spectrum","ref": "MS"}
  ]},
Derived Spectral Data File
- type:
free text
- definition
The name of the derived spectral data file (the .mzML file itself)
- example value:
  {"value": "Person30_RBC_elder_NEG.mzML"}
Detector
- type:
  cv term
- definition
  The detector used in the mass spectrometer (child of MS:1000026)
- example value:
  {"accession": "http://purl.obolibrary.org/obo/MS_1000253",
   "name": "electron multiplier","ref": "MS"}
Inlet type
- type
  cv term
- definition
  The type of inlet (child of MS:1000007)
- example value:
  {"accession": "http://purl.obolibrary.org/obo/MS_1000057",
   "name": "electrospray inlet","ref": "MS"}
Instrument
- type
  cv term
- definition
  The mass spectrometry instrument used for the scan
- example value:
  {"accession": "http://purl.obolibrary.org/obo/MS_1000449",
   "name": "LTQ Orbitrap","ref": "MS"}
Instrument manufacturer
- type
  cv term
- definition
  The manufacturer of the MS instrument
- example value:
  {"accession": "http://purl.obolibrary.org/obo/MS_1000483",
   "name": "Thermo Fisher Scientific instrument model","ref": "MS"}
Instrument serial number
- type
  free text
- definition
  The serial number of the MS instrument
 "value": "1057B"
Instrument software
- type
  cv term
- definition
  The software used by the MS instrument
- example value:
  {"accession": "http://purl.obolibrary.org/obo/MS_1000532",
   "name": "Xcalibur","ref": "MS"}
Instrument software version
- type:
  free text
- definition
  The version of the Instrument software
- example value:
  {"value": "2.2"}
Ion source
- type
  cv term
- definition
  The method by which gas phase ions are generated from the sample.
- example value:
  {"accession": "http://purl.obolibrary.org/obo/MS_1000073",
   "name": "electrospray ionization","ref": "MS"}
MS Assay Name
- type
  free text
- definition
  The name of the MS Assay (mzML file name w/o extension)
- example value
  {"value": "Person30_RBC_elder_NEG"}
Mass analyzer
- type
  cv term
- definition
  How ions are separated according to their mass-to-charge ratio
- example value
  {"accession": "http://purl.obolibrary.org/obo/MS_1000083",
   "name": "radial ejection linear ion trap","ref": "MS"}
Native spectrum identifier format
- type
  cv term
- definition
  The format of the native spectrum identifier
- example value
  {"accession": "http://purl.obolibrary.org/obo/MS_1000768",
   "name": "Thermo nativeID format","ref": "MS"}
Number of scans
- type:
  int
- definition
  The number of scans performed
- example value
  {"value": 1073}
Raw Spectral Data File
- type
  free text
- definition
  The raw spectral data file (as extracted from the .mzML)
- example value
  {"value": "20120627_SAM00533_RBC_NEG.RAW"}
Raw data file format
- type
  cv term
- definition
  The format of the raw data file
- example value
  {"accession": "http://purl.obolibrary.org/obo/MS_1000563",
   "name": "Thermo RAW format","ref": "MS"}
Sample Name
- type
  free text
- definition
  The name of the sample (populated as the .mzML filename w/o extension)
- example value
  {"value": "Person30_RBC_elder_NEG"}
Scan m/z range
- type
  free text
- definition
  The isolation window m/z range used during the scans
- example value
  {"value": "50-1945"}
Scan polarity
- type
  free text
- definition
  The polarity of the scan (can be 'positive', 'negative', 'alternating' or 'n/a')
- example value
  {"value": "negative"}

Note

It would be preferable for this to be a cv term, but while the PSI-MS ontology provides positive scan and a negative scan term, it doesn’t provide any alternating scan term although referencing it among the possible scan polarity values. A request to add alternating scan to the MS ontology will probably be made.

Time range
- type:
  free text
- definition
  The range of scan start times of all the scans
- example value
  {"value": "0.0061-30.0042"}

imzML

All the aforementioned (if relevant), and the following

Binary file checksum type
- type:
  cv term w/ value
- definition
  The value and type of the checksum used to check the binary file.
- example value:
  {"accession":"IMS:1000091", "name": "ibd SHA-1", "ref": "IMS"}
Detector mode
- type
  list of cv terms
- definition
  The mode the detector was set on during the scans
- example value
  {"entry_list": [
     {"accession": "http://purl.obolibrary.org/obo/MS_1000118",
      "name": "pulse counting","ref": "MS"},
  ]},
High-res image
- type
  free text
- definition
  The name of the high-res image file
- example value
  {"value": "BRB04W.ndpi"}

Warning

Although the default value for this term will always be extracted as "name_of_the_imzML_file".ndpi, mzml2isa will always try to find that file in the parsed folder. Which means, if it can find it, nothing will be extracted for that value.

Ibd binary type
- type
  cv term
- definition
  The type of data contained in the ibd binary file
- example value
  {"accession": "IMS:1000031",
   "name": "processed","ref": "IMS"}
Line scan direction
- type
  cv term
- definition
  The direction in which the lines of the sample were scanned
- example value
  {"accession": "IMS:1000491",
   "name": "linescan left right","ref": "IMS"}
Linescan sequence
- type
  cv term
- definition
  The direction of the succession of the assembling of the linescans.
- example value
  {"accession": "IMS:1000401",
   "name": "top down","ref": "IMS"}
Max count of pixel x
- type
  cv term w/ value
- definition
  The max length of the x axis among all scans
- example value
  {"accession": "IMS:1000042","name": "max count of pixel x",
   "ref": "IMS","value": "103"}
Max count of pixel y
- type
  cv term w/ value
- definition
  The max length of the y axis among all scans
- example value
  {"accession": "IMS:1000043","name": "max count of pixel y",
   "ref": "IMS","value": "58"}
Max dimension x
- type
  cv term w/ value w/ unit
- definition
  The size of the largest scanned line of x axis
- example value
  {"accession": "IMS:1000044",
   "name": "max dimension x", "ref": "IMS",
   "value": "9095"
   "unit": {"accession": "UO:0000017",
            "name": "micrometer","ref": "UO"} }
Max dimension y
- type
  cv term w/ value w/ unit
- definition
  The size of the largest scanned line of y axis
- example value
  {"accession": "IMS:1000044",
   "name": "max dimension x", "ref": "IMS",
   "value": "8900"
   "unit": {"accession": "UO:0000017",
            "name": "micrometer","ref": "UO"} }
Pixel size x
- type
  cv term w/ value w/ unit
- definition
  The size of the x dimension of a pixel
- example value
  {"accession": "IMS:1000046",
   "name": "pixel size x","ref": "IMS",
   "value": "85",
    "unit": {"accession": "UO:0000017",
             "name": "micrometer","ref": "UO"} }
Pixel size y
- type
  cv term w/ value w/ unit
- definition
  The size of the y dimension of a pixel
- example value
  {"accession": "IMS:1000047",
   "name": "pixel size y","ref": "IMS",
   "value": "85",
    "unit": {"accession": "UO:0000017",
             "name": "micrometer","ref": "UO"} }
Scan pattern
- type
  cv term
- definition
  The pattern how the image was scanned (child of IMS:1000041)
- example value
  {"accession": "IMS:1000413",
   "name": "flyback","ref": "IMS"}
Scan type
- type
  cv term
- definition
  The direction in which the lines were scanned (child of IMS:1000048)
- example value
  {"accession": "IMS:1000480",
   "name": "horizontal line scan", "ref": "IMS"}
Solvent
- type
  cv term w/ value
- definition
  The solvent used on the sample
- example value
  {"accession": "IMS:1001211",
   "name": "solvent","ref": "IMS",
   "value": "methanol"}

Note

That parameter was only seen once, and it was a free text value. It would be better if this was a cv term, so changing the solvent column in the ISA file may be considered.

Solvent flowrate
- type
  cv term w/ value w/ unit
- definition
  The flowrate of the solvent on the sample
- example value
  {"accession": "IMS:1001213",
   "name": "solvent flowrate", "ref": "IMS",
   "value": "1.5"
   "unit": {"accession": "IMS:1000131",
            "name": "milliliter per minute","ref": "IMS"} }
Spectrum representation
- type
  list of cv terms
- definition
  The way in which the spectra are reprensented
- example value
  {"entry_list": [
     {"accession": "MS:1000127",
      "name": "centroid spectrum","ref": "MS"}
  ]}
Target material
- type
  free text
- definition
  The material that is targeted by the IMS instrument
- example value
  {"accession": "IMS:1000202",
   "name": "target material","ref": "IMS",
   "value": "Glas"}
Universally unique identifier
- type
  cv term w/ value
- definition
  The UUID of the IBD binary file
- example value
  {"accession": "IMS:1000080",
   "name": "universally unique identifier","ref": "IMS",
   "value": "{6E2F1092-F43A-4169-94CB-61DD5A61047E}"}

Warning

The following items are being extracted with a redundant cv term, which we’ll probably get rid of in the future: