diff --git a/src/ontology/modules/data-transformations.owl b/src/ontology/modules/data-transformations.owl index 110a5ba4..682dd8da 100644 --- a/src/ontology/modules/data-transformations.owl +++ b/src/ontology/modules/data-transformations.owl @@ -22,6 +22,12 @@ + + + + + + @@ -40,6 +46,12 @@ + + + + + + @@ -69,6 +81,12 @@ + + + + + + + + + + + + + + + + + + + + + + + @@ -109,12 +145,12 @@ The process of deriving a data item from an image data set using computer algorithms. The produced data item can be an image data set, data measurement, or any other data item. - https://orcid.org/0000-0001-9625-1899 "William D. Duncan" - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" - https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" - https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" - https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" + https://orcid.org/0000-0001-9625-1899 "William D. Duncan" + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" + https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" https://github.com/obi-ontology/obi/issues/1481 image data set analysis @@ -139,23 +175,134 @@ - A Fourier transform of raw "k-space" data produced into an image data set that represents the anatomical structure of the tissue examined. + A Fourier transform of raw "k-space" data produced into an image data set that represents the anatomical structure of the tissue examined. A process that transforms raw magnetic resonance image data from an NMR/MRI machine into a reconstructed magnetic resonance image data set. - https://orcid.org/0000-0001-9625-1899 "William D. Duncan" - https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" - https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" - https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" - https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" - https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" + https://orcid.org/0000-0001-9625-1899 "William D. Duncan" + https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" + https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" + https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" + https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" + https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" https://github.com/obi-ontology/obi/issues/1481 raw magnetic resonance image data set reconstruction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + tandem mass spectrometry analysis + Sebastian Duesing + A mass spectrometry analysis in which the data being analyzed is the result of a tandem mass spectrometry assay. + https://github.com/obi-ontology/obi/issues/1684 + tandem mass spectrometry analysis + + + + + + + + + + + + + + + + + + + + + + + + + + + + + liquid chromatography mass spectrometry analysis + Sebastian Duesing + A mass spectrometry analysis in which the data being analyzed is the result of a liquid chromatography mass spectrometry assay. + https://github.com/obi-ontology/obi/issues/1684 + liquid chromatrography mass spectrometry analysis + + + + + + + + + + + + + + + + + + + + + + + + + + + + + liquid chromatography tandem mass spectrometry analysis + Sebastian Duesing + A mass spectrometry analysis in which the data being analyzed is the result of a liquid chromatography tandem mass spectrometry assay. + https://github.com/obi-ontology/obi/issues/1684 + liquid chromatography-tandem mass spectrometry analysis + + + + + + + + + + diff --git a/src/ontology/modules/devices.owl b/src/ontology/modules/devices.owl index b5b64c16..4e31ff82 100644 --- a/src/ontology/modules/devices.owl +++ b/src/ontology/modules/devices.owl @@ -1043,7 +1043,6 @@ PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01072 - check on definition ! solvent mixer @@ -1964,7 +1963,6 @@ PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01055 - chromatography device, check on definition ! column cartridge @@ -2192,7 +2190,6 @@ PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01054 - check on definition ! column cartridger @@ -2223,7 +2220,6 @@ PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01065 - chromatography device, check on definition ! needle assembly @@ -6949,12 +6945,12 @@ - Illumina Infinium MethylationEPIC BeadChip + Illumina Infinium MethylationEPIC v1.0 BeadChip An Illumina methylation BeadChip which is an array that interrogates ~ 850,000 methylation sites per sample at single-nucleotide resolution. Person: Chris Stoeckert, Jason Hilton http://www.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/humanmethylationepic-data-sheet-1070-2015-008.pdf - Illumina Infinium MethylationEPIC BeadChip + Illumina Infinium MethylationEPIC v1.0 BeadChip @@ -9136,6 +9132,20 @@ + + + + + Illumina Infinium MethylationEPIC v2.0 BeadChip + An Illumina methylation BeadChip that targets 935,000 methylation sites per sample at single-nucleotide resolution. + Sebastian Duesing + https://www.illumina.com/products/by-type/microarray-kits/infinium-methylation-epic.html + https://github.com/obi-ontology/obi/issues/1665 + Illumina Infinium MethylationEPIC v2.0 BeadChip + + + + diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index aac49a88..234b7a23 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -22422,6 +22422,18 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + A clinical data item that quantifies the severity of a person's fatigue as measured by a 20-item self-report instrument. + Sebastian Duesing + https://pubmed.ncbi.nlm.nih.gov/7636775/ DOI: 10.1016/0022-3999(94)00125-o + multidimensional fatigue inventory score + + + + diff --git a/src/ontology/templates/data-transformations.tsv b/src/ontology/templates/data-transformations.tsv index 3a3d1c03..69694ebf 100644 --- a/src/ontology/templates/data-transformations.tsv +++ b/src/ontology/templates/data-transformations.tsv @@ -2,3 +2,6 @@ ontology ID label editor preferred term has curation status alternative term def ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| A definition SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A term tracker item CLASS_TYPE C % C has_specified_input some % C has_specified_output some % C achieves_planned_objective some % C % OBI:0003355 image data set analysis The process of deriving a data item from an image data set using computer algorithms. The produced data item can be an image data set, data measurement, or any other data item. https://orcid.org/0000-0001-9676-7377 ""Alexander D. Bartnik""|https://orcid.org/0000-0001-9990-8331 ""Alexander D. Diehl""|https://orcid.org/0000-0001-9625-1899 ""William D. Duncan""|https://orcid.org/0000-0002-2104-0568 ""Lucas M. Serra""|https://orcid.org/0000-0002-7245-3450 ""Lauren M. Wishnie""|https://orcid.org/0000-0002-9821-4132 ""Mackenzie T. Smith"" https://github.com/obi-ontology/obi/issues/1481 subclass data transformation image data set OBI:0003356 raw magnetic resonance image data set reconstruction A process that transforms raw magnetic resonance image data from an NMR/MRI machine into a reconstructed magnetic resonance image data set. A Fourier transform of raw ""k-space"" data produced into an image data set that represents the anatomical structure of the tissue examined. https://orcid.org/0000-0001-9676-7377 ""Alexander D. Bartnik""|https://orcid.org/0000-0001-9990-8331 ""Alexander D. Diehl""|https://orcid.org/0000-0001-9625-1899 ""William D. Duncan""|https://orcid.org/0000-0002-2104-0568 ""Lucas M. Serra""|https://orcid.org/0000-0002-7245-3450 ""Lauren M. Wishnie""|https://orcid.org/0000-0002-9821-4132 ""Mackenzie T. Smith"" https://github.com/obi-ontology/obi/issues/1481 equivalent image data set analysis raw magnetic resonance image data set reconstructed magnetic resonance image data set +OBI:0003647 tandem mass spectrometry analysis tandem mass spectrometry analysis A mass spectrometry analysis in which the data being analyzed is the result of a tandem mass spectrometry assay. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1684 equivalent mass spectrometry analysis ('data item' and is_specified_output_of some 'tandem mass spectrometry assay') +OBI:0003648 liquid chromatrography mass spectrometry analysis liquid chromatography mass spectrometry analysis A mass spectrometry analysis in which the data being analyzed is the result of a liquid chromatography mass spectrometry assay. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1684 equivalent mass spectrometry analysis ('data item' and is_specified_output_of some 'liquid chromatography mass spectrometry assay') +OBI:0003649 liquid chromatography-tandem mass spectrometry analysis liquid chromatography tandem mass spectrometry analysis A mass spectrometry analysis in which the data being analyzed is the result of a liquid chromatography tandem mass spectrometry assay. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1684 equivalent mass spectrometry analysis ('data item' and is_specified_output_of some 'liquid chromatography-tandem mass spectrometry') diff --git a/src/ontology/templates/devices.tsv b/src/ontology/templates/devices.tsv index 4443e87b..9e1b4426 100644 --- a/src/ontology/templates/devices.tsv +++ b/src/ontology/templates/devices.tsv @@ -345,7 +345,7 @@ OBI:0002109 Human 6x630K CGH Whole Genome Tiling Array ready for release Nimble OBI:0002128 Illumina Genome Analyzer Illumina Genome Analyzer pending final vetting Illumina Genome Analyzer I A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. http://www.illumina.com/technology/next-generation-sequencing/solexa-technology.html Person: Chris Stoeckert, Jason Hilton DNA sequencer OBI:0002129 Illumina HiSeq X Ten Illumina HiSeq X Ten pending final vetting HiSeq X Ten A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. http://www.illumina.com/systems/hiseq-x-sequencing-system/system.html Person: Chris Stoeckert, Jason Hilton, Sagar Jain, Richard Scheuermann DNA sequencer OBI:0002130 Illumina Infinium Omni5Exome-4 Kit Illumina Infinium Omni5Exome-4 Kit pending final vetting An Illumina BeadChip which is an array that interrogates over 4.3 million whole-genome variants for genotyping and copy number variation. http://www.illumina.com/products/by-type/microarray-kits/infinium-omni5-exome.html Person: Chris Stoeckert, Jason Hilton Illumina BeadChip -OBI:0002131 Illumina Infinium MethylationEPIC BeadChip Illumina Infinium MethylationEPIC BeadChip pending final vetting An Illumina methylation BeadChip which is an array that interrogates ~ 850,000 methylation sites per sample at single-nucleotide resolution. http://www.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/humanmethylationepic-data-sheet-1070-2015-008.pdf Person: Chris Stoeckert, Jason Hilton Illumina methylation BeadChip +OBI:0002131 Illumina Infinium MethylationEPIC v1.0 BeadChip Illumina Infinium MethylationEPIC v1.0 BeadChip pending final vetting An Illumina methylation BeadChip which is an array that interrogates ~ 850,000 methylation sites per sample at single-nucleotide resolution. http://www.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/humanmethylationepic-data-sheet-1070-2015-008.pdf Person: Chris Stoeckert, Jason Hilton Illumina methylation BeadChip OBI:0002192 Leica Peloris rapid tissue processor Leica Peloris rapid tissue processor ready for release An automatic tissue processor that is a dual retort tissue processor manufactured by the Leica company to provide fast, high quality tissue processing for histology laboratories. http://drp8p5tqcb2p5.cloudfront.net/fileadmin/downloads_lbs/Leica%20PELORIS/User%20Manuals/Leica_Peloris_manual_EN.pdf Chris Stoeckert, Helena Ellis NCI BBRB automatic tissue processor OBI:0002194 Microm Ergostar HM200 Microm Ergostar HM200 ready for release A microtome that is manufactured by Microm and uses a vertical cutting stroke common to all rotary microtomes engaged by a horizontal sliding movement. An operating arm replaces the handwheel and is attached to both sides of the instrument for greater convenience to permit control of sectioning from the left or right. http://www.ultra-medical.com/Microm-Ergostar-HM200-Microtome/en Chris Stoeckert, Helena Ellis NCI BBRB microtome OBI:0002195 microtome blade microtome blade ready for release A device that is the part of a microtome used to slice specimens to a desired thickness. https://en.wikipedia.org/wiki/Microtome Chris Stoeckert, Helena Ellis NCI BBRB device @@ -468,6 +468,7 @@ OBI:0003494 Advantage Chikungunya IgM Card kit An assay kit that is manufactu OBI:0003550 odor baited CDC light trap human odour baited light trap A CDC light trap that uses odorous gas from a human being as an attractant, by pumping it from the room where the human being sleeps into the trap. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1654 Centers for Disease Control and Prevention light trap OBI:0003551 resting clay pot trap resting clay pot catch A resting arthropod trap that consists of a container composed primarily of clay. John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1651 resting arthropod trap OBI:0003606 Illumina NextSeq 1000 NextSeq 1000 A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells. https://www.illumina.com/systems/sequencing-platforms/nextseq-1000-2000.html Sebastian Duesing GENEPIO https://github.com/obi-ontology/obi/issues/1711 subclass DNA sequencer Illumina +OBI:0003650 Illumina Infinium MethylationEPIC v2.0 BeadChip Illumina Infinium MethylationEPIC v2.0 BeadChip An Illumina methylation BeadChip that targets 935,000 methylation sites per sample at single-nucleotide resolution. https://www.illumina.com/products/by-type/microarray-kits/infinium-methylation-epic.html Sebastian Duesing https://github.com/obi-ontology/obi/issues/1665 Illumina methylation BeadChip OBI:0400005 A10-Analyzer A10-Analyzer ready for release A A10 is a flow_cytometer_analyser manufactured by Apogee. It uses an arc lamp as a light source, with choices of 75W Xe, 75W Xe/Hg or 100W Hg arc lamps. It has filters and collectors for up to three fluorescent parameters and two scatter parameters. It uses analog electronics. The A10 can be used for measuring the properties of individual cells. http://www.apogeeflow.com/flow_cytometry_products.htm John Quinn flow cytometer analyzer OBI:0400006 A40-MiniFCM A40-MiniFCM ready for release A A40-MiniFCM is a flow_cytometer_analyser that allows for the choice of one of four lasers (375nm, 405nm,488nm, 532nm, 635nm), and PMTs and filters for collecting up to four parameters. It uses digital electronics. A military version of this cytometer is available as well. The A40-MiniFCM is geared towards the most demanding applications such as archaea, bacteria and large virus. http://www.apogeeflow.com/flow_cytometry_products.htm John Quinn flow cytometer analyzer OBI:0400007 analog-to-digital converter analog-to-digital converter metadata incomplete A2D|A-D An analog-to-digital_converter is an instrument that converts an infinite resolution analog signal to a finite resolution digital signal. http://en.wiktionary.org/wiki/Analog-to-Digital_Converter The analog to digital converter transformed the analog output from the photomultiplier tube to a digital signal for collection. John Quinn|Melanie Courtot device signal conversion function