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: