From 55e81c76fc93313e5fd8ac8bd79fa65dcaac57cd Mon Sep 17 00:00:00 2001 From: Joshua Klein Date: Fri, 28 Oct 2022 11:59:20 -0400 Subject: [PATCH] Generate OWL file --- psi-ms.owl | 369 ++++++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 367 insertions(+), 2 deletions(-) diff --git a/psi-ms.owl b/psi-ms.owl index dc2638b..2c1b7fa 100644 --- a/psi-ms.owl +++ b/psi-ms.owl @@ -34,13 +34,13 @@ xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#" xmlns:caloha-reqs-vetted="http://purl.obolibrary.org/obo/caloha-reqs-vetted#"> - + * MS:$sequence(7,0,9999999)$ * PEFF:$sequence(7,0,9999999)$ OBO-Edit 2.3.1 - 21:09:2022 11:38 + 26:10:2022 11:38 MS 1.2 Joshua Klein @@ -18799,6 +18799,7 @@ + @@ -18871,6 +18872,7 @@ + @@ -47893,6 +47895,12 @@ + + + + + + Attribute of a single peptide-spectrum match. MS MS:1002345 @@ -66531,6 +66539,7 @@ + @@ -66561,6 +66570,7 @@ + @@ -66597,6 +66607,7 @@ + @@ -67915,6 +67926,12 @@ + + + + + + A user-provided name for a user-defined value describing a trait not covered by an existing controlled vocabulary term. This term should be used sparingly, preferring existing terms that describe the specific concept. Should be used with MS:1003276 to provide the attribute's value MS MS:1003275 @@ -67933,6 +67950,42 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A user-provided value for a user-defined name describing a trait not covered by an existing controlled vocabulary term. This term should be used sparingly, preferring existing terms that describe the specific concept. Should be used with MS:1003275 to provide the attribute's name MS MS:1003276 @@ -68326,6 +68379,318 @@ + + + + + Summary statistics of an attribute among all replicates that are aggregated to generate this spectrum. + MS + MS:1003295 + summary statistics of replicates + + + + + Summary statistics of an attribute among all replicates that are aggregated to generate this spectrum. + PSI:PI + + + + + + + + + + + + + + + The number of replicate spectra used during the aggregation process that originate from a specified source (e.g. a file, a dataset, a sample type, etc.). This term must appear in a group alongside a source term, which is one of: 'ProteomeXchange accession number', 'constituent spectrum file', or 'sample name' + MS + MS:1003296 + number of replicates spectra used from source + + + + + The number of replicate spectra used during the aggregation process that originate from a specified source (e.g. a file, a dataset, a sample type, etc.). This term must appear in a group alongside a source term, which is one of: 'ProteomeXchange accession number', 'constituent spectrum file', or 'sample name' + PSI:PI + + + + + + + + + A cross reference to another spectrum that is a replicate spectrum of the same analyte and contributes to the generation of this aggregated spectrum. + MS + MS:1003297 + contributing replicate spectrum + + + + + A cross reference to another spectrum that is a replicate spectrum of the same analyte and contributes to the generation of this aggregated spectrum. + PSI:PI + + + + + + + + + + + + + + A list of cross references to contributing replicate spectra in the same library, in the form of library spectrum keys. + MS + MS:1003298 + contributing replicate spectrum keys + + + + + A list of cross references to contributing replicate spectra in the same library, in the form of library spectrum keys. + PSI:PI + + + + + + + + + + + + + + A list of cross references to contributing replicate spectra, in the form of PSI Universal Spectrum Identifiers. + MS + MS:1003299 + contributing replicate spectrum USI + + + + + A list of cross references to contributing replicate spectra, in the form of PSI Universal Spectrum Identifiers. + PSI:PI + + + + + + + + + + + + + + Result of a comparison of a spectrum to another spectrum, usually to assess the plausibility that the two spectra originate from the same analyte. + MS + MS:1003300 + spectrum match + + + + + Result of a comparison of a spectrum to another spectrum, usually to assess the plausibility that the two spectra originate from the same analyte. + PSI:PI + + + + + + + + + Result of a comparison of an observed fragment ion spectrum to the theoretically predicted fragmentation pattern of a peptide sequence, to assess the plausibility that the observed spectrum originates from the putative peptide sequence. + PSM + MS + MS:1003301 + peptide-spectrum match + + + + + Result of a comparison of an observed fragment ion spectrum to the theoretically predicted fragmentation pattern of a peptide sequence, to assess the plausibility that the observed spectrum originates from the putative peptide sequence. + PSI:PI + + + + + + + + + Result of a comparison of an observed fragment ion spectrum to another observed fragment ion spectrum, to assess the plausibility that two spectra originate from the same analyte, e.g., in spectral library searching and spectrum clustering. + SSM + MS + MS:1003302 + spectrum-spectrum match + + + + + Result of a comparison of an observed fragment ion spectrum to another observed fragment ion spectrum, to assess the plausibility that two spectra originate from the same analyte, e.g., in spectral library searching and spectrum clustering. + PSI:PI + + + + + + + + + + + + + + + A measure of how similar two spectra are, based on the features of the spectra (the locations and intensities of peaks) alone. + MS + MS:1003303 + spectral similarity + + + + + A measure of how similar two spectra are, based on the features of the spectra (the locations and intensities of peaks) alone. + PSI:PI + + + + + + + + + + + + + + + The dot (inner) product of two vectorized spectra divided by the product of their vector norms. It ranges from 0 (orthogonal vectors) to 1 (collinear vectors). Also known as cosine similarity. + cosine similarity + MS + MS:1003304 + spectral dot product + + + + + The dot (inner) product of two vectorized spectra divided by the product of their vector norms. It ranges from 0 (orthogonal vectors) to 1 (collinear vectors). Also known as cosine similarity. + PSI:PI + + + + + + + + + + + + + + + The Euclidean distance between a pair of points representing two vectorized spectra in high-dimensional space. + MS + MS:1003305 + spectral Euclidean distance + + + + + The Euclidean distance between a pair of points representing two vectorized spectra in high-dimensional space. + PSI:PI + + + + + + + + + + + + + + + The number of peaks with closely matching m/z values that are common to two spectra. + MS + MS:1003306 + shared peak count + + + + + The number of peaks with closely matching m/z values that are common to two spectra. + PSI:PI + + + + + + + + + + + + + + + The angle subtended by two vectorized spectra in high-dimensional space. It is equal to the 1 - (2 * inverse cosine of the spectral dot product) / pi. + MS + MS:1003307 + normalized spectral angle + + + + + The angle subtended by two vectorized spectra in high-dimensional space. It is equal to the 1 - (2 * inverse cosine of the spectral dot product) / pi. + https://doi.org/10.1074/mcp.O113.036475 + + + + + + + + + + + + + + + The Pearson's rho statistic between a pair of points representing two vectorized spectra. + MS + MS:1003308 + spectral Pearson correlation + + + + + The Pearson's rho statistic between a pair of points representing two vectorized spectra. + PSI:PI + + + +