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From: Jones, A. <And...@li...> - 2016-06-16 08:47:17
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Hi all, We have a scheduled call at 4pm UK time today. I will unfortunately have to leave at 4.20 but let's have a brief catch up as to where we are and rattle through some of the open issues. Best wishes Andy Numbers: + UK: 0808 109 5644 + US: 877-420-0272 + Belgium: 0800 509 80 + Germany: 0800 101 2079 + Switzerland: 0800 000 860 + Generic international: +44 (0) 20 8322 2500 (UK number) Access code: 297427 # |
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From: Julian U. <not...@gi...> - 2016-06-15 16:45:06
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This bug seems to be related to these lines in the mzIdentML inside the analysisSoftware, which should be correct: `<ContactRole contact_ref="ORG_MSL">` ` <Role>` ` <cvParam cvRef="PSI-MS" accession="MS:1001267" name="software vendor"></cvParam>` ` </Role>` `</ContactRole>` --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/47#issuecomment-226247146 |
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From: Julian U. <not...@gi...> - 2016-06-15 11:09:47
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I get a reproducible crash of the validator (1.4.18) when trying to validate the attached file:[pia_testMzIdentML.mzId.gz](https://github.com/HUPO-PSI/mzIdentML/files/315992/pia_testMzIdentML.mzId.gz The file is erroneous, but still the validator should not crash. After the last uncatched exception, the GUI stay where it is, pretending to do something. This is the output on the console: > $ java -Xmx8G -jar mzIdentMLValidator-1.4.18-SNAPSHOT.jar > BrendaTissueOBO.obo > gene_ontology.obo > psi-ms.obo > PSI-MOD.obo > pato.obo > unimod.obo > unit.obo > > > There were errors validating against the XML schema: > > - ValidatorMessage{message='Non-fatal XML Parsing error detected on line 20215 > Error message: cvc-complex-type.2.4.b: The content of element 'AnalysisCollection' is not complete. One of '{"http://psidev.info/psi/pi/mzIdentML/1.1":SpectrumIdentification}' is expected.', level=ERROR, context=null, rule=null} > - ValidatorMessage{message='Non-fatal XML Parsing error detected on line 41189 > Error message: Key 'FK_SoftwareContact' with value 'ORG_MSL' not found for identity constraint of element 'MzIdentML'.', level=ERROR, context=null, rule=null} > - ValidatorMessage{message='Non-fatal XML Parsing error detected on line 20216 > Error message: cvc-complex-type.2.4.b: The content of element 'AnalysisProtocolCollection' is not complete. One of '{"http://psidev.info/psi/pi/mzIdentML/1.1":SpectrumIdentificationProtocol}' is expected.', level=ERROR, context=null, rule=null} > - ValidatorMessage{message='Non-fatal XML Parsing error detected on line 20261 > Error message: cvc-complex-type.4: Attribute 'id' must appear on element 'SpectrumIdentificationList'.', level=ERROR, context=null, rule=null} > Number of rules to check: 35 > Exception in thread "Thread-1" java.lang.IllegalStateException: Could not instantiate reference resolver: uk.ac.ebi.jmzidml.xml.jaxb.resolver.ContactRoleRefResolver > at uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller.listeners.RawXMLListener.referenceResolving(RawXMLListener.java:192) > at uk.ac.ebi.jmzidml.xml.jaxb.unmarshaller.listeners.RawXMLListener.afterUnmarshal(RawXMLListener.java:55) > at com.sun.xml.internal.bind.v2.runtime.unmarshaller.Loader.fireAfterUnmarshal(Loader.java:221) > at com.sun.xml.internal.bind.v2.runtime.unmarshaller.StructureLoader.leaveElement(StructureLoader.java:276) > at com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallingContext.endElement(UnmarshallingContext.java:585) > at com.sun.xml.internal.bind.v2.runtime.unmarshaller.SAXConnector.endElement(SAXConnector.java:165) > at org.xml.sax.helpers.XMLFilterImpl.endElement(XMLFilterImpl.java:570) > at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(AbstractSAXParser.java:609) > at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(XMLDocumentFragmentScannerImpl.java:1783) > at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2970) > at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:606) > at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:118) > at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:510) > at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:848) > at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:777) > at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141) > at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1213) > at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:643) > at org.xml.sax.helpers.XMLFilterImpl.parse(XMLFilterImpl.java:357) > at com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.unmarshal0(UnmarshallerImpl.java:243) > at com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.unmarshal(UnmarshallerImpl.java:221) > at com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.unmarshal(UnmarshallerImpl.java:273) > at uk.ac.ebi.jmzidml.xml.io.MzIdentMLObjectIterator.next(MzIdentMLObjectIterator.java:88) > at uk.ac.ebi.jmzidml.xml.io.MzIdentMLObjectIterator.next(MzIdentMLObjectIterator.java:41) > at psidev.psi.pi.validator.MzIdentMLValidator.checkElementCvMapping(MzIdentMLValidator.java:1143) > at psidev.psi.pi.validator.MzIdentMLValidator.applyCVMappingRules(MzIdentMLValidator.java:779) > at psidev.psi.pi.validator.MzIdentMLValidator.doValidationWork(MzIdentMLValidator.java:511) > at psidev.psi.pi.validator.MzIdentMLValidator.startValidation(MzIdentMLValidator.java:429) > at psidev.psi.pi.validator.MzIdentMLValidatorGUI$4.construct(MzIdentMLValidatorGUI.java:681) > at psidev.psi.pi.validator.swingworker.SwingWorker.lambda$new$1(SwingWorker.java:138) > at java.lang.Thread.run(Thread.java:745) --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/47 |
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From: Gerhard M. <not...@gi...> - 2016-06-15 08:49:52
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Shouldn't it be accession = Prot C.1 inside PDH 1.1 of PAG 3 (in the left figure) ? --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/24#issuecomment-226126585 |
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From: Gerhard M. <not...@gi...> - 2016-06-14 15:06:56
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Removed the units from the FDR and q-value terms in version 3.90.0 of psi-ms.obo --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/39#issuecomment-225911986 |
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From: Gerhard M. <not...@gi...> - 2016-06-14 15:06:14
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Removed the units from the FDR and q-value terms in version 3.90.0 of psi-ms.obo --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/35#issuecomment-225911794 |
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From: mayerg97 <ger...@ru...> - 2016-06-14 15:02:08
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Dear proteomics community, attached there's the new version 3.90.0 of the psi-ms.obo file containing new terms for the annotation of cross-linking files, for supplemental activation and for the OpenXQuest search engine. New CV terms in version 3.90.0 of psi-ms.obo: ============================================= ************ terms for cross-linking annotation [Term] id: MS:1002675 name: cross-linking result details def: "This subsection describes terms which can describe details of cross-linking results." [PSI:PI] relationship: part_of MS:1001000 ! spectrum interpretation [Term] id: MS:1002676 name: protein-pair-level global FDR def: "Estimation of the global false discovery rate of proteins-pairs in cross-linking experiments." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002675 ! cross-linking result details relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive [Term] id: MS:1002677 name: residue-pair-level global FDR def: "Estimation of the global false discovery rate of residue-pairs in cross-linking experiments." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002675 ! cross-linking result details relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive ************ Terms for supplemental activation [Term] id: MS:1002678 name: supplemental higher energy beam-type collision-induced dissociation def: "A supplemental collision-induced dissociation process wherein the projectile ion has the translational energy higher than approximately 1000 eV." [PSI:MS] is_a: MS:1000422 ! beam-type collision-induced dissociation [Term] id: MS:1002679 name: supplemental collision-induced dissociation def: "The dissociation of an ion after supplemental collisional excitation." [PSI:MS] is_a: MS:1000044 ! dissociation method [Term] id: MS:1002680 name: supplemental collision energy def: "Energy for an ion experiencing supplemental collision with a stationary gas particle resulting in dissociation of the ion." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000510 ! precursor activation attribute relationship: has_units UO:0000266 ! electronvolt ************ OpenXQuest search engine scores [Term] id: MS:1002681 name: OpenXQuest:combined score def: "OpenXQuest's combined score for a cross-link spectrum match." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! search engine specific score for PSMs is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better [Term] id: MS:1002682 name: OpenXQuest:xcorr xlink def: "OpenXQuest's cross-correlation of cross-linked ions subscore." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! search engine specific score for PSMs is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better [Term] id: MS:1002683 name: OpenXQuest:xcorr common def: "OpenXQuest's cross-correlation of unlinked ions subscore." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! search engine specific score for PSMs is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better [Term] id: MS:1002684 name: OpenXQuest:match-odds def: "OpenXQuest's match-odds subscore." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! search engine specific score for PSMs is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better relationship: has_domain MS:1002306 ! value greater than zero [Term] id: MS:1002685 name: OpenXQuest:intsum def: "OpenXQuest's sum of matched peak intensity subscore." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! search engine specific score for PSMs is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better relationship: has_domain MS:1002306 ! value greater than zero [Term] id: MS:1002686 name: OpenXQuest:wTIC def: "OpenXQuest's weighted percent of total ion current subscore." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! search engine specific score for PSMs is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive Changed CV terms in version 3.90.0 of psi-ms.obo: ================================================= ************ Removed the units UO:0000166 and UO:0000187 from the following FDR- and q-value terms [Term] id: MS:1001250 name: local FDR def: "Result of quality estimation: the local FDR at the current position of a sorted list." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001092 ! peptide identification confidence metric is_a: MS:1001198 ! protein identification confidence metric [Term] id: MS:1001868 name: distinct peptide-level q-value def: "Estimation of the q-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs, possibly with different mass modifications, mapping to the same sequence have been collapsed to one entry)." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002484 ! peptide-level statistical threshold relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive [Term] id: MS:1001869 name: protein-level q-value def: "Estimation of the q-value for proteins." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001198 ! protein identification confidence metric relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive [Term] id: MS:1002354 name: PSM-level q-value def: "Estimation of the q-value for peptide spectrum matches." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002347 ! PSM-level identification confidence metric relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive [Term] id: MS:1002373 name: protein group-level q-value def: "Estimation of the q-value for protein groups." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002348 ! protein group-level identification confidence metric relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive 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/> RUB Logo ANNOUNCEMENT de.NBI summer school September 2016: *Analysis of Mass-Spectrometric Data - * *Big Data Bioinformatics in Proteomics and Metabolomics* http://www.denbi.de/index.php/11-training-cat/95-lss2016 |
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From: F. G. <not...@gi...> - 2016-06-14 13:56:58
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I have update the example file. @edeutsch can you please re-run the validator. Thanks. Fawaz --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/35#issuecomment-225888665 |
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From: F. G. <not...@gi...> - 2016-06-14 13:56:55
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I have update the example file. @edeutsch can you please re-run the validator. Thanks. Fawaz --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/38#issuecomment-225888639 |
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From: F. G. <not...@gi...> - 2016-06-14 13:56:52
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I have update the example file. @edeutsch can you please re-run the validator. Thanks. Fawaz --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/39#issuecomment-225888597 |
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From: F. G. <not...@gi...> - 2016-06-14 13:56:42
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I have update the example file. @edeutsch can you please re-run the validator. Thanks. Fawaz --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/40#issuecomment-225888550 |
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From: andrewrobertjones <not...@gi...> - 2016-06-14 12:50:43
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Agree all FDR and q-value terms should not have any units - @germa can you check if there are other similar terms e.g. evalues and pvalues, PEP etc that have units. I don't think any of these should. thanks --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/35#issuecomment-225870875 |
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From: andrewrobertjones <not...@gi...> - 2016-06-14 12:49:57
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@germa The units should also be removed from this one: id: MS:1001250 name: local FDR def: "Result of quality estimation: the local FDR at the current position of a sorted list." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001092 ! peptide identification confidence metric is_a: MS:1001198 ! protein identification confidence metric relationship: has_units UO:0000166 ! parts per notation unit relationship: has_units UO:0000187 ! percent --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/38#issuecomment-225870643 |
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From: andrewrobertjones <not...@gi...> - 2016-06-14 12:48:11
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@germa Please can we update the q-value term (below). Both of the units are wrong, I'm pretty sure there are no suitable units for a q-value. Thanks Andy [Term] id: MS:1002354 name: PSM-level q-value def: "Estimation of the q-value for peptide spectrum matches." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002347 ! PSM-level identification confidence metric relationship: has_units UO:0000166 ! parts per notation unit relationship: has_units UO:0000187 ! percent relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/39#issuecomment-225870228 |
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From: Mathias W. <not...@gi...> - 2016-06-14 11:39:02
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I second that. :+1: --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/42#issuecomment-225855640 |
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From: Mathias W. <not...@gi...> - 2016-06-14 11:37:11
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depending on #45 should also resolve #43 --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/pull/46#issuecomment-225855307 |
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From: Mathias W. <not...@gi...> - 2016-06-14 11:36:16
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should resolve #37 --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/pull/46#issuecomment-225855135 |
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From: Mathias W. <not...@gi...> - 2016-06-12 11:02:57
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You can view, comment on, or merge this pull request online at: https://github.com/HUPO-PSI/mzIdentML/pull/46 -- Commit Summary -- * Update OpenxQuest_example.mzid -- File Changes -- M examples/1_2examples/crosslinking/OpenxQuest_example.mzid (308) -- Patch Links -- https://github.com/HUPO-PSI/mzIdentML/pull/46.patch https://github.com/HUPO-PSI/mzIdentML/pull/46.diff --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/pull/46 |
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From: Mathias W. <not...@gi...> - 2016-06-11 13:06:52
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As discussed and agreed in the mzid call: to avoid bloat of cv, bloat of mzid files with extended annotation information, and allow for extended ion annotation (e.g. cross-linking) IonType can contain zero or more userParam elements. ``` xsd <xsd:documentation>In case more information about the ions annotation has to be conveyed, that has no fit in FragmentArray. Note: It is suggested that the value attribute takes the form of a list of the same size as FragmentArray values. However, there is no formal encoding and it cannot be expeceted that other software will process or impart that information properly.</xsd:documentation> ```  You can view, comment on, or merge this pull request online at: https://github.com/HUPO-PSI/mzIdentML/pull/45 -- Commit Summary -- * Added userParams to IonType -- File Changes -- M schema/mzIdentML1.2.0-candidate.xsd (7) -- Patch Links -- https://github.com/HUPO-PSI/mzIdentML/pull/45.patch https://github.com/HUPO-PSI/mzIdentML/pull/45.diff --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/pull/45 |
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From: Gerhard M. <not...@gi...> - 2016-06-10 09:59:24
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Yes in the .obo file there is X\!Tandem used, but in our data files one must use X!Tandem. The .obo file needs this backslash in the .obo file since otherwise the BioPortal validator will complain. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/38#issuecomment-225143190 |
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From: Gerhard M. <not...@gi...> - 2016-06-10 09:27:27
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By some reasons, which I forgot, we decided to use at first onls the minimal version (Issue #20). I created now an .obo file out of that Excel sheet. @Lutz: Can you double check, if all is encoded ok (I added a definition for each cross-linker). --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/44#issuecomment-225136077 |
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From: Eric D. <not...@gi...> - 2016-06-09 20:10:46
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I agree. I believe that ! with no \ is the correct way to encode it in mzIdentML. I suspect the presence of the \! in the OBO file is an OBO syntax thing that should not be replicated to mzIdentML. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/38#issuecomment-225011702 |
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From: Harald B. <not...@gi...> - 2016-06-09 20:05:38
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@edeutsch We have 'X!Tandem:expect' and 'X!Tandem xml format' in our PeptideShaker mzid 1.2 example file, but I don't think you get the same error for our file? (At least Gerhard's validator does not.) So could be some special formatting issue? We don't do anything special on our side though regarding the '!'. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/38#issuecomment-225010322 |
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From: Eric D. <not...@gi...> - 2016-06-09 17:42:32
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What is the distinction between: XLMOD-1.0.0.csv XLMOD.csv It would be nice to have a proper OBO file for my validator, but I could code up handling for csv. What does the Java validator do? XLMOD-1.0.0.csv shows this: XL:00001,Xlink:BS3,2,138.06807961,"(K,S,T,Y,Protein N-term)&(K,S,T,Y,Protein N-term)" while XLMOD.csv shows this: XL:00001,BS3,bis(sulfosuccinimidyl)suberate,https://www.thermofisher.com/order/catalog/product/21580,Xlink:BS3,BS3,2,138.06807961,138.16,"C8 H10 O2", "(K,S,T,Y,Protein N-term)&(K,S,T,Y,Protein N-term)" The latter seems to be the more complete one? I hope we're leaving the "Xlink:" prefix behind as not needed? --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/44 |
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From: Eric D. <not...@gi...> - 2016-06-09 17:38:30
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ERROR: cvParam retention time should have units, but it does not!
ERROR: cvParam search engine specific score for PSMs has a value, but it should not!
WARNING: cvParam product ion intensity has a legal unit MS:1000131 but its name 'MS:1000131' should be 'number of detector counts'!
WARNING: CV term MS:100xxxx ('crosslink ion category') is not in the cv
WARNING: MS:1002510 should be 'cross-link acceptor' instead of 'cross-link receiver'
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