From: mayerg97 <ger...@ru...> - 2016-07-01 10:03:34
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format-version: 1.2 data-version: releases/2016-07-01 ontology: xl date: 01:07:2016 11:46 saved-by: Gerhard Mayer auto-generated-by: OBO-Edit 2.3.1 default-namespace: XL remark: namespace: XL remark: version: 1.0.0_rc1 remark: release date: 2016-07-01 remark: coverage: cross-linking reagents remark: creator: Lutz Fischer <lfischer <-at-> staffmail.ed.ac.uk> remark: creator: Gerhard Mayer <mayerg97 <-at-> rub.de> remark: This work is licensed under the Creative Commons Attribution 3.0 Unported License. remark: To view a copy of this license, visit http://creativecommons.org/licenses/by/3.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA. [Typedef] id: part_of name: part_of is_transitive: true [Typedef] id: is_labelled name: is_labelled [Typedef] id: is_partially_reacted name: is_partially_reacted [Typedef] id: has_property name: has_property [Term] id: XL:00000 name: Proteomics Standards Initiative cross-linking controlled vocabulary def: "Proteomics Standards Initiative cross-linking controlled vocabulary." [PSI:XL] [Term] id: XL:00001 name: cross-linking entity def: "Entity relevant to the domain of cross-linking in proteomics." [PSI:XL] relationship: part_of XL:00000 ! Proteomics Standards Initiative cross-linking controlled vocabulary [Term] id: XL:00002 name: cross-linker related PTM def: "A cross-linker reagent with one reactive group." [PSI:XL] relationship: part_of XL:00000 ! Proteomics Standards Initiative cross-linking controlled vocabulary [Term] id: XL:00003 name: label transfer reagent def: "A cross-linker acting as label (e.g. biotin) transfer reagent." [PSI:XL] relationship: part_of XL:00000 ! Proteomics Standards Initiative cross-linking controlled vocabulary [Term] id: XL:00004 name: cross-linker def: "Compound that can link two or more polymer chains." [PSI:XL] is_a: XL:00001 ! cross-linking entity [Term] id: XL:00005 name: homofunctional cross-linker def: "A cross-linker reagent with identical reactive groups at each end of the spacer arm." [PSI:XL] is_a: XL:00004 ! cross-linker [Term] id: XL:00006 name: heterofunctional cross-linker def: "A cross-linker reagent with at least two different reactive groups." [PSI:XL] is_a: XL:00004 ! cross-linker [Term] id: XL:00007 name: photoreactive cross-linker def: "A cross-linker reagent that becomes reactive when exposed to ultraviolet or visible light." [PSI:XL] synonym: "non-selective cross-linker" EXACT [PSI:XL] is_a: XL:00004 ! cross-linker [Term] id: XL:00008 name: zero-length cross-linker def: "A cross-linker reagent causing direct conjugation without becoming part of the final cross-link between the target molecules." [PSI:XL] is_a: XL:00004 ! cross-linker [Term] id: XL:00010 name: deuterium-labelled def: "Indicates that a cross-linker is deuterium-labelled." [PSI:XL] relationship: part_of XL:00001 ! cross-linking entity [Term] id: XL:00011 name: hydrolyzed def: "Indicates that a cross-linker is hydrolyzed." [PSI:XL] relationship: part_of XL:00001 ! cross-linking entity [Term] id: XL:00012 name: amidated def: "Indicates that a cross-linker is amidated." [PSI:XL] relationship: part_of XL:00001 ! cross-linking entity [Term] id: XL:00013 name: membrane permeable def: "Indicates that a cross-linker is membrane permeable." [PSI:XL] relationship: part_of XL:00001 ! cross-linking entity [Term] id: XL:00014 name: water soluble def: "Indicates that a cross-linker is water soluble." [PSI:XL] relationship: part_of XL:00001 ! cross-linking entity [Term] id: XL:00101 name: BS3 def: "Bis(sulfosuccinimidyl)suberate." [PSI:XL, CAS:82436-77-9, PubChem_Compound:6097991] property_value: reactionSites: "2" xsd:nonNegativeInteger property_value: monoisotopicMass: "138.06807961" xsd:double property_value: specificities: "(K,S,T,Y,Protein N-term)&(K,S,T,Y,Protein N-term)" xsd:string property_value: spacerLength: "11.4" xsd:double is_a: XL:00005 ! homofunctional cross-linker relationship: has_property XL:00014 ! water soluble [Term] id: XL:00102 name: DSS def: "Disuccinimidyl suberate." [PSI:XL, CAS:68528-80-3, PubChem_Compound:100658] property_value: reactionSites: "2" xsd:nonNegativeInteger property_value: monoisotopicMass: "138.06807961" xsd:double property_value: specificities: "(K,S,T,Y,Protein N-term)&(K,S,T,Y,Protein N-term)" xsd:string property_value: spacerLength: "11.4" xsd:double is_a: XL:00005 ! homofunctional cross-linker relationship: has_property XL:00013 ! membrane_permeable [Term] id: XL:00103 name: DSS-d4 def: "Deuterium-labelled disuccinimidyl 2,2,7,7-suberate." [PSI:XL, PubChem_Compound:91757798] property_value: reactionSites: "2" xsd:nonNegativeInteger property_value: monoisotopicMass: "142.093186586" xsd:double property_value: specificities: "(K,S,T,Y,Protein N-term)&(K,S,T,Y,Protein N-term)" xsd:string property_value: spacerLength: "11.4" xsd:double is_a: XL:00005 ! homofunctional cross-linker relationship: is_labelled XL:00010 ! deuterium-labelled [Term] id: XL:00104 name: DSS-d12 def: "Deuterium-labelled disuccinimidyl 2,2,3,3,4,4,5,5,6,6,7,7-suberate." [PSI:XL] property_value: reactionSites: "2" xsd:nonNegativeInteger property_value: monoisotopicMass: "150.143400538" xsd:double property_value: specificities: "(K,S,T,Y,Protein N-term)&(K,S,T,Y,Protein N-term)" xsd:string property_value: spacerLength: "11.4" xsd:double is_a: XL:00005 ! homofunctional cross-linker relationship: is_labelled XL:00010 ! deuterium-labelled [Term] id: XL:00105 name: BS3-d4 def: "Deuterium-labelled (bis(sulfosuccinimidyl) 2,2,7,7-suberate-d4)." [PSI:XL, PubChem_Compound:91757801] property_value: reactionSites: "2" xsd:nonNegativeInteger property_value: monoisotopicMass: "142.093186586" xsd:double property_value: specificities: "(K,S,T,Y,Protein N-term)&(K,S,T,Y,Protein N-term)" xsd:string property_value: spacerLength: "11.4" xsd:double is_a: XL:00005 ! homofunctional cross-linker relationship: is_labelled XL:00010 ! deuterium-labelled [Term] id: XL:00106 name: BS2G def: "Bis(sulfosuccinimidyl) glutarat." [PSI:XL, PubChem_Compound:91757794] property_value: reactionSites: "2" xsd:nonNegativeInteger property_value: monoisotopicMass: "96.0211294" xsd:double property_value: specificities: "(K,S,T,Y,Protein N-term)&(K,S,T,Y,Protein N-term)" xsd:string property_value: spacerLength: "7.7" xsd:double is_a: XL:00005 ! homofunctional cross-linker [Term] id: XL:00107 name: DSG def: "Disuccinimidyl glutarate." [PSI:XL, CAS:79642-50-5, PubChem_Compound:4432628] property_value: reactionSites: "2" xsd:nonNegativeInteger property_value: monoisotopicMass: "96.0211294" xsd:double property_value: specificities: "(K,S,T,Y,Protein N-term)&(K,S,T,Y,Protein N-term)" xsd:string property_value: spacerLength: "7.7" xsd:double is_a: XL:00005 ! homofunctional cross-linker relationship: has_property XL:00013 ! membrane_permeable [Term] id: XL:00108 name: DSG-d4 def: "Deuterium-labelled disuccinimidyl 2,2,4,4-glutarate." [PSI:XL, PubChem_Compound:91757797] property_value: reactionSites: "2" xsd:nonNegativeInteger property_value: monoisotopicMass: "146.118293562" xsd:double property_value: specificities: "(K,S,T,Y,Protein N-term)&(K,S,T,Y,Protein N-term)" xsd:string property_value: spacerLength: "7.7" xsd:double is_a: XL:00005 ! homofunctional cross-linker relationship: is_labelled XL:00010 ! deuterium-labelled [Term] id: XL:00109 name: BS2G-d4 def: "Deuterium-labelled bis(sulfosuccinimidyl) 2,2,4,4-glutarate." [PSI:XL, PubChem_Compound:91757799] property_value: reactionSites: "2" xsd:nonNegativeInteger property_value: monoisotopicMass: "100.046236376" xsd:double property_value: specificities: "(K,S,T,Y,Protein N-term)&(K,S,T,Y,Protein N-term)" xsd:string property_value: spacerLength: "7.7" xsd:double is_a: XL:00005 ! homofunctional cross-linker relationship: is_labelled XL:00010 ! deuterium-labelled [Term] id: XL:00110 name: Disulfide def: "Disulfide." [PSI:XL] property_value: reactionSites: "2" xsd:nonNegativeInteger property_value: monoisotopicMass: "-2.01565007" xsd:double property_value: specificities: "(C)&(C)" xsd:string is_a: XL:00005 ! homofunctional cross-linker [Term] id: XL:00111 name: EDC def: "1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride." [PSI:XL, CAS:25952-53-8, PubChem_Compound:2723939] property_value: reactionSites: "2" xsd:nonNegativeInteger property_value: monoisotopicMass: "-18.01056027" xsd:double property_value: specificities: "(K,S,T,Y,Protein N-term)&(E,D,Protein C-term)" xsd:string is_a: XL:00008 ! zero-length cross-linker [Term] id: XL:00112 name: BDP-NHP def: "Biotin Aspartate Proline n-hydroxyphthalamide." [PSI:XL] property_value: reactionSites: "2" xsd:nonNegativeInteger property_value: monoisotopicMass: "1241.469925525" xsd:double property_value: specificities: "(K,Protein N-term)&(K,Protein N-term)" xsd:string is_a: XL:00003 ! label transfer agent [Term] id: XL:01000 name: hydrolyzed BS3 def: "Hydrolyzed bis(sulfosuccinimidyl)suberate." [PSI:XL] property_value: reactionSites: "1" xsd:nonNegativeInteger property_value: monoisotopicMass: "156.07864431" xsd:double property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string property_value: spacerLength: "11.4" xsd:double is_a: XL:00005 ! homofunctional cross-linker relationship: is_partially_reacted XL:00011 ! hydrolyzed [Term] id: XL:01001 name: amidated BS3 def: "Amidated bis(sulfosuccinimidyl)suberate." [PSI:XL] property_value: reactionSites: "1" xsd:nonNegativeInteger property_value: monoisotopicMass: "155.094628715" xsd:double property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string property_value: spacerLength: "11.4" xsd:double is_a: XL:00005 ! homofunctional cross-linker relationship: is_partially_reacted XL:00012 ! amidated [Term] id: XL:01002 name: hydrolyzed DSS def: "Hydrolyzed disuccinimidyl suberate." [PSI:XL] property_value: reactionSites: "1" xsd:nonNegativeInteger property_value: monoisotopicMass: "156.07864431" xsd:double property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string property_value: spacerLength: "11.4" xsd:double is_a: XL:00005 ! homofunctional cross-linker relationship: is_partially_reacted XL:00011 ! hydrolyzed [Term] id: XL:01003 name: amidated DSS def: "Amidated disuccinimidyl suberate." [PSI:XL] property_value: reactionSites: "1" xsd:nonNegativeInteger property_value: monoisotopicMass: "155.094628715" xsd:double property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string property_value: spacerLength: "11.4" xsd:double is_a: XL:00005 ! homofunctional cross-linker relationship: is_partially_reacted XL:00012 ! amidated [Term] id: XL:01004 name: hydrolyzed DSS-d4 def: "Deuterium-labelled hydrolyzed disuccinimidyl 2,2,7,7-suberate." [PSI:XL] property_value: reactionSites: "1" xsd:nonNegativeInteger property_value: monoisotopicMass: "160.1037416836" xsd:double property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string property_value: spacerLength: "11.4" xsd:double is_a: XL:00005 ! homofunctional cross-linker relationship: is_partially_reacted XL:00011 ! hydrolyzed [Term] id: XL:01005 name: amidated DSS-d4 def: "Deuterium-labelled amidated disuccinimidyl 2,2,7,7-suberate." [PSI:XL] property_value: reactionSites: "1" xsd:nonNegativeInteger property_value: monoisotopicMass: "159.1197260886" xsd:double property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string property_value: spacerLength: "11.4" xsd:double is_a: XL:00005 ! homofunctional cross-linker relationship: is_partially_reacted XL:00012 ! amidated relationship: is_labelled XL:00010 ! deuterium-labelled [Term] id: XL:01006 name: hydrolyzed DSS-d12 def: "Deuterium-labelled hydrolyzed disuccinimidyl 2,2,3,3,4,4,5,5,6,6,7,7-suberate." [PSI:XL] property_value: reactionSites: "1" xsd:nonNegativeInteger property_value: monoisotopicMass: "168.153965238" xsd:double property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string property_value: spacerLength: "11.4" xsd:double is_a: XL:00005 ! homofunctional cross-linker relationship: is_partially_reacted XL:00011 ! hydrolyzed relationship: is_labelled XL:00010 ! deuterium-labelled [Term] id: XL:01007 name: amidated DSS-d12 def: "Deuterium-labelled amidated disuccinimidyl 2,2,3,3,4,4,5,5,6,6,7,7-suberate." [PSI:XL] property_value: reactionSites: "1" xsd:nonNegativeInteger property_value: monoisotopicMass: "167.169949643" xsd:double property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string property_value: spacerLength: "11.4" xsd:double is_a: XL:00005 ! homofunctional cross-linker relationship: is_partially_reacted XL:00012 ! amidated relationship: is_labelled XL:00010 ! deuterium-labelled [Term] id: XL:01008 name: hydrolyzed BS3-d4 def: "Deuterium-labelled hydrolyzed bis(sulfosuccinimidyl) 2,2,7,7-suberate." [PSI:XL] property_value: reactionSites: "1" xsd:nonNegativeInteger property_value: monoisotopicMass: "160.103751286" xsd:double property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string property_value: spacerLength: "11.4" xsd:double property_value: spacerLength: "11.4" xsd:double is_a: XL:00005 ! homofunctional cross-linker relationship: is_partially_reacted XL:00011 ! hydrolyzed relationship: is_labelled XL:00010 ! deuterium-labelled [Term] id: XL:01009 name: amidated BS3-d4 def: "Deuterium-labelled amidated bis(sulfosuccinimidyl) 2,2,7,7-suberate." [PSI:XL] property_value: reactionSites: "1" xsd:nonNegativeInteger property_value: monoisotopicMass: "159.119735691" xsd:double property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string property_value: spacerLength: "11.4" xsd:double is_a: XL:00005 ! homofunctional cross-linker relationship: is_partially_reacted XL:00012 ! amidated relationship: is_labelled XL:00010 ! deuterium-labelled [Term] id: XL:01010 name: hydrolyzed BS2G def: "Hydrolyzed bis(sulfosuccinimidyl) glutarate." [PSI:XL] property_value: reactionSites: "1" xsd:nonNegativeInteger property_value: monoisotopicMass: "114.0316941" xsd:double property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string property_value: spacerLength: "7.7" xsd:double is_a: XL:00005 ! homofunctional cross-linker relationship: is_partially_reacted XL:00011 ! hydrolyzed [Term] id: XL:01011 name: amidated BS2G def: "Amidated bis(sulfosuccinimidyl) glutarate." [PSI:XL] property_value: reactionSites: "1" xsd:nonNegativeInteger property_value: monoisotopicMass: "113.047678505" xsd:double property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string property_value: spacerLength: "7.7" xsd:double is_a: XL:00005 ! homofunctional cross-linker relationship: is_partially_reacted XL:00012 ! amidated [Term] id: XL:01012 name: hydrolyzed DSG def: "Hydrolyzed disuccinimidyl glutarate." [PSI:XL] property_value: reactionSites: "1" xsd:nonNegativeInteger property_value: monoisotopicMass: "114.0316941" xsd:double property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string property_value: spacerLength: "7.7" xsd:double is_a: XL:00004 ! cross-linker relationship: is_partially_reacted XL:00011 ! hydrolyzed [Term] id: XL:01013 name: amidated DSG def: "Amidated disuccinimidyl glutarate." [PSI:XL] property_value: reactionSites: "1" xsd:nonNegativeInteger property_value: monoisotopicMass: "113.047678505" xsd:double property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string property_value: spacerLength: "7.7" xsd:double is_a: XL:00005 ! homofunctional cross-linker relationship: is_partially_reacted XL:00012 ! amidated [Term] id: XL:01014 name: hydrolyzed DSG-d4 def: "Deuterium-labelled amidated disuccinimidyl 2,2,4,4-glutarate." [PSI:XL] property_value: reactionSites: "1" xsd:nonNegativeInteger property_value: monoisotopicMass: "164.128858262" xsd:double property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string property_value: spacerLength: "7.7" xsd:double is_a: XL:00005 ! homofunctional cross-linker relationship: is_partially_reacted XL:00011 ! hydrolyzed relationship: is_labelled XL:00010 ! deuterium-labelled [Term] id: XL:01015 name: amidated DSG-d4 def: "Deuterium-labelled hydrolyzed disuccinimidyl 2,2,4,4-glutarate." [PSI:XL] property_value: reactionSites: "1" xsd:nonNegativeInteger property_value: monoisotopicMass: "163.144842667" xsd:double property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string property_value: spacerLength: "7.7" xsd:double is_a: XL:00005 ! homofunctional cross-linker relationship: is_partially_reacted XL:00012 ! amidated relationship: is_labelled XL:00010 ! deuterium-labelled [Term] id: XL:01016 name: hydrolyzed BS2G-d4 def: "Deuterium-labelled hydrolyzed bis(sulfosuccinimidyl) 2,2,4,4-glutarate." [PSI:XL] property_value: reactionSites: "1" xsd:nonNegativeInteger property_value: monoisotopicMass: "118.056801076" xsd:double property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string property_value: spacerLength: "7.7" xsd:double is_a: XL:00005 ! homofunctional cross-linker relationship: is_partially_reacted XL:00011 ! hydrolyzed relationship: is_labelled XL:00010 ! deuterium-labelled [Term] id: XL:01017 name: amidated BS2G-d4 def: "Deuterium-labelled amidated bis(sulfosuccinimidyl) 2,2,4,4-glutarate." [PSI:XL] property_value: reactionSites: "1" xsd:nonNegativeInteger property_value: monoisotopicMass: "117.072785481" xsd:double property_value: specificities: "(K,S,T,Y,Protein N-term)" xsd:string property_value: spacerLength: "7.7" xsd:double is_a: XL:00005 ! homofunctional cross-linker relationship: is_partially_reacted XL:00012 ! amidated relationship: is_labelled XL:00010 ! deuterium-labelled [Term] id: XL:01017 name: BDP-NHP-stump def: "Biotin Aspartate Proline n-hydroxyphthalimide-stump." [PSI:XL] property_value: reactionSites: "1" xsd:nonNegativeInteger property_value: monoisotopicMass: "197.032422395" xsd:double property_value: specificities: "(K,Protein N-term)" xsd:string is_a: XL:00003 ! label transfer agent |
From: Jones, A. <And...@li...> - 2016-07-01 10:13:56
Attachments:
image001.jpg
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For me it is fine to start with a clean slate, since it hasn’t been widely distributed or used yet. Best wishes Andy From: mayerg97 [mailto:ger...@ru...] Sent: 01 July 2016 11:03 To: psi...@li...; psi...@li...; psi...@li... Subject: [Psidev-ms-vocab] new Cross-Linker ontology XLMOD.obo Hi all, together with Lutz I developed a new proposal of our cross-linker ontology. We have now more structuring and possibilities to model the properties of the cross-linkers. Since we put a lot of new intermediate terms for structuring, some ID's changed, but I think it's still ok at the moment to restart with a clean state, since until now nowhere beside of our .mzid 1.2 examples the ontology is used so far. So we just must update our cross-linker example files. Is that ok? Best regards, Gerhard -- -------------------------------------------------------------------- Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER PhD student Medizinisches Proteom-Center DEPARTMENT Medical Bioinformatics Building ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum Fon +49 (0)234 32-21006 | Fax +49 (0)234 32-14554 E-mail ger...@ru...<mailto:ger...@ru...> www.medizinisches-proteom-center.de<http://www.medizinisches-proteom-center.de> [cid:image001.jpg@01D1D389.A27A7650] |
From: Mathias W. <wa...@in...> - 2016-07-01 11:34:49
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So if you create a new XLMOD.obo it's fine with me regarding restructuring hierarchy and numeration etc; provided the linkers themselves present now do not disappear. best, mths ----- Original Message ----- From: "Andy Jones" <And...@li...> To: psi...@li..., psi...@li..., psi...@li... Sent: Friday, 1 July, 2016 12:13:47 PM Subject: Re: [Psidev-ms-dev] [Psidev-ms-vocab] new Cross-Linker ontology XLMOD.obo For me it is fine to start with a clean slate, since it hasn’t been widely distributed or used yet. Best wishes Andy From: mayerg97 [mailto:ger...@ru...] Sent: 01 July 2016 11:03 To: psi...@li...; psi...@li...; psi...@li... Subject: [Psidev-ms-vocab] new Cross-Linker ontology XLMOD.obo Hi all, together with Lutz I developed a new proposal of our cross-linker ontology. We have now more structuring and possibilities to model the properties of the cross-linkers. Since we put a lot of new intermediate terms for structuring, some ID's changed, but I think it's still ok at the moment to restart with a clean state, since until now nowhere beside of our .mzid 1.2 examples the ontology is used so far. So we just must update our cross-linker example files. Is that ok? Best regards, Gerhard -- -------------------------------------------------------------------- Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER PhD student Medizinisches Proteom-Center DEPARTMENT Medical Bioinformatics Building ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum Fon +49 (0)234 32-21006 | Fax +49 (0)234 32-14554 E-mail ger...@ru... www.medizinisches-proteom-center.de ------------------------------------------------------------------------------ Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape _______________________________________________ Psidev-ms-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev |