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From: Prof. R. J. L. <rob...@uw...> - 2006-04-10 19:15:57
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Maren and Burkhard, I note your responses ... > Unfortunately, informed guesses are not 21 CFR 11 compliant (no accurate copy of records). It is the task of the technique definition groups to make sure the required AnIML elements can be filled. Yes. Technique definitions should not have fields marked as mandatory where it's likely that the data will be difficult or impossible to obtain. But I note that pathlength is REQUIRED for IR. This can't be obtained when you do a KBr or nujol mull, surely? Robert -- Prof. Robert J. Lancashire mailto:rob...@uw... Department of Chemistry Tel (876) 512 3026 University of the West Indies, Kingston 7 Fax (876) 9771835 Mona Campus, JAMAICA. http://wwwchem.uwimona.edu.jm/chrl.html |
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From: Burkhard S. <b_...@us...> - 2006-04-10 20:11:05
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Robert, > But I note that pathlength is REQUIRED for IR. > This can't be obtained when you do a KBr or nujol mull, surely? thanks for pointing this out. I have filed this as bug report #1467948 for the IR Technique Definition. The IR Technique review team will look into that. https://sourceforge.net/tracker/index.php?func=detail&aid=1467948&group_id=76803&atid=548317 Burkhard |
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From: Peter M. <Pet...@re...> - 2006-04-10 21:48:57
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At 02:14 PM 4/10/2006 -0500, you wrote: >Maren and Burkhard, > >I note your responses ... > > > Unfortunately, informed guesses are not 21 CFR 11 compliant (no > accurate copy of records). It is the task of the technique definition > groups to make sure the required AnIML elements can be filled. > >Yes. Technique definitions should not have fields marked as mandatory >where it's likely that the data will be difficult or impossible to obtain. > > >But I note that pathlength is REQUIRED for IR. >This can't be obtained when you do a KBr or nujol mull, surely? OR If you use an ATR accessory OR If you use an IRRAS accessory OR If you do diffuse or specular reflectance Peter >Robert > > > > >-- >Prof. Robert J. Lancashire mailto:rob...@uw... >Department of Chemistry Tel (876) 512 3026 >University of the West Indies, Kingston 7 Fax (876) 9771835 >Mona Campus, JAMAICA. http://wwwchem.uwimona.edu.jm/chrl.html > > >------------------------------------------------------- >This SF.Net email is sponsored by xPML, a groundbreaking scripting language >that extends applications into web and mobile media. Attend the live webcast >and join the prime developer group breaking into this new coding territory! >http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 >_______________________________________________ >Animl-develop mailing list >Ani...@li... >https://lists.sourceforge.net/lists/listinfo/animl-develop ============================================================================== Peter J. Melling Ph.D. Remspec Corporation Ph. 508 248-1462 Fax. 508 248-1463 www.remspec.com ============================================================================== |
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From: Burkhard S. <b_...@us...> - 2006-04-12 05:44:01
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Peter, I've added your comment to the bug report. Burkhard >> But I note that pathlength is REQUIRED for IR. >> This can't be obtained when you do a KBr or nujol mull, surely? > > OR > > If you use an ATR accessory > > OR > > If you use an IRRAS accessory > > OR > > If you do diffuse or specular reflectance > > > Peter |
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From: Prof. R. J. L. <rob...@uw...> - 2006-04-12 14:57:29
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Burkhard et al, Information for IR that should be required is whether the spectrum was recorded as gas phase, KBr disc/k, parafin/nujol mull, solution, etc including the techniques mentioned by Peter below. If ATR, IRRAS, then there may well be other parameters that should be recorded and set as required as well. If a simple mull, what plates were used? NaCl, CsI, KRS5 etc. Once again you face the problem of converting legacy data which may not be an issue when processing new spectra. In JCAMP-DX there is a distinction made between TEXT and STRING values. TEXT essentially says it can be anything STRING represents pre-defined key words so ##TITLE= is text ##DATA TYPE is string with for example INFRARED SPECTRUM pre-defined and published in the protocol. I think things like SAMPLEID should have a pre-defined string to say this is the SAMPLE or BACKGROUND or REFERENCE or BLANK whatever to aid ease of processing. For an IR: Things like SampleState with text as solid is probably not sufficient whereas if it was some defined string that might be more meaningful. If you look at one of the example files from Anh Dao for example SampleName is polycarbonatepellet samplestate is solid It may be possible to decide how the experiment was performed but I think it could be nailed down much tighter. A few more points to ponder over .... Robert they say a good way to learn about something is to have to teach it. You could expand this to say that a good way to try to come up with a decent protocol is to have to write a program to read it back again! on 12/04/2006 12:43 AM Burkhard Schaefer said the following: > Peter, > > I've added your comment to the bug report. > > Burkhard > >>> But I note that pathlength is REQUIRED for IR. >>> This can't be obtained when you do a KBr or nujol mull, surely? >> >> OR >> >> If you use an ATR accessory >> >> OR >> >> If you use an IRRAS accessory >> >> OR >> >> If you do diffuse or specular reflectance >> >> >> Peter > > > > ------------------------------------------------------- > This SF.Net email is sponsored by xPML, a groundbreaking scripting language > that extends applications into web and mobile media. Attend the live > webcast > and join the prime developer group breaking into this new coding territory! > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 > _______________________________________________ > Animl-develop mailing list > Ani...@li... > https://lists.sourceforge.net/lists/listinfo/animl-develop -- Prof. Robert J. Lancashire mailto:rob...@uw... Department of Chemistry Tel (876) 512 3026 University of the West Indies, Kingston 7 Fax (876) 9771835 Mona Campus, JAMAICA. http://wwwchem.uwimona.edu.jm/chrl.html |
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From: Amanda C. <af...@ab...> - 2006-04-20 11:07:57
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> In JCAMP-DX there is a distinction made between TEXT and STRING > values. > TEXT essentially says it can be anything > STRING represents pre-defined key words > > so ##TITLE= is text > ##DATA TYPE is string with for example INFRARED SPECTRUM pre-defined and > published in the protocol. > > I think things like SAMPLEID should have a pre-defined string > to say this is the SAMPLE or BACKGROUND or REFERENCE or BLANK > whatever to aid ease of processing. > > For an IR: > Things like SampleState with text as solid is probably not sufficient > whereas if it was some defined string that might be more meaningful. For all of the terms in any XML-based document we should be using the principles of the Semantic Web, which have been around for years now. That is, the terms you use within an AnIML document should be defined in an ontology, and which ontology you've used for any term should be stated. This gives the flexibility to use any term that you need, from any accessible ontology, but the term is still well defined, so that processing software can make use of it. The existing ontologies for science are still under development, but a standard such as AnIML should be making use of their potential. See for example: http://msi-ontology.sourceforge.net/index.htm Amanda -- Amanda Clare http://users.aber.ac.uk/afc/ 1851 Research Fellow Tel: +44 (0)1970 628406 Fax: +44 (0)1970 628536 Dept. of Computer Science, University of Wales, Aberystwyth, SY23 3DB |
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From: <Mar...@gs...> - 2006-04-20 13:17:55
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AnIML has a process for obtaining semantic definitions; that's what the Technique definitions are for. Each technique is in charge of creating its own semantic vocabulary based on Maren Fiege's gleanings from JCAMP dictionaries as a core. The understanding of the AnIML XML core structure and the semantics in the Technique definitions is key to using AnIML correctly. It is true that the Techniques are incomplete, so this is a great place for newcomers to get involved. Mark (chair of the mass spectrometry Technique group that hasn't even met yet) |
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From: Prof. R. J. L. <rob...@uw...> - 2006-04-20 14:31:21
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Amanda and Mark,
It would seem my original email was unclear since I do recognise the
importance of data definitions and have worked on producing these
for JCAMP-DX for many years with the latest just published for
ESR/EPR/EMR.
My difficulty was in trying to determine whether some of the
elements being suggested for use should have come from a standard
set of terms or whether they could be free text.
When I first wrote, I was having trouble with
<SampleSet>
<Sample sampleID="...." derived="false">
followed later by entries under
<MeasurementData>
<SamplesUsed>
<SampleRef sampleID= "..." role="SampleMeasurement" purpose="consumed" />
Given that there may be additional information given under the original
section of <Sample> such as name, owner, MP, BP CAS, INCHI
it would seem important when trying to write software to read this information
to be able to identify AT THAT STAGE that
the information in a particular sampleset belongs to the actual
sample being measured and is not from the blank or reference etc.
Hence my question as to whether sampleID should be a reserved string
and not free text. Alternatively it would be possible to have
the ROLE descriptor there as long as the term "SampleMeasurement"
is a recognised keyword for ALL techniques and the alternatives
were also recognised as such by ALL techniques as well e.g
blank, solvent, reference etc.
Are these defined somewhere for ALL techniques? If so where do
I find them?
I hope this request is clearer?
Thanks
Robert
on 20/04/2006 08:17 AM Mar...@gs... said the following:
>
> AnIML has a process for obtaining semantic definitions; that's what the
> Technique definitions are for. Each technique is in charge of creating
> its own semantic vocabulary based on Maren Fiege's gleanings from JCAMP
> dictionaries as a core. The understanding of the AnIML XML core
> structure and the semantics in the Technique definitions is key to using
> AnIML correctly. It is true that the Techniques are incomplete, so this
> is a great place for newcomers to get involved.
>
> Mark (chair of the mass spectrometry Technique group that hasn't even
> met yet)
--
Prof. Robert J. Lancashire mailto:rob...@uw...
Department of Chemistry Tel (876) 512 3026
University of the West Indies, Kingston 7 Fax (876) 9771835
Mona Campus, JAMAICA. http://wwwchem.uwimona.edu.jm/chrl.html
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From: <Mar...@wa...> - 2006-05-09 08:56:38
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Hi Robert, > Information for IR that should be required is whether the spectrum=20 > was recorded as gas phase, KBr disc/k, parafin/nujol mull, solution, etc = including the > techniques mentioned by Peter below. If ATR, IRRAS, then there may well > be other parameters that should be recorded and set as required as well. I added this as a to do in the bug tracker. > In JCAMP-DX there is a distinction made between TEXT and STRING > values. > TEXT essentially says it can be anything > STRING represents pre-defined key words We depict this in the technique definitions using enumerations. The=20 principle is the same. Mit freundlichen Gr=FC=DFen / Best regards Maren.=20 Dr. Maren Fiege Senior Product Manager =20 Waters GmbH Europaallee 27, D-50226 Frechen, Germany Tel.+49 2234 9207 - 0 Fax +49 2234 9207-99 http://www.waters.com/informatics=20 |
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From: Prof. R. J. L. <rob...@uw...> - 2006-04-10 21:52:08
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Burkhard, in conversion of JCAMP-DX files to AnIML I am concerned about RESOLUTION as well since this is NOT required in JCAMP-DX so will not be present in thousands of files already in existence. Our PE FTIR machines can be set at 1,2 or 4 cm-1 resolution so even then I am not always sure what was the setting when the info was recorded. What should go into the field in the AnIML file exported from a JCAMP-DX file when it is given as REQUIRED? Another problem I have.... I am attaching a section of a file from Anh ============================================================== <AnIML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="animl-core.xsd" xmlns:ds="http://www.w3.org/2000/09/xmldsig#" version="1.0"> <SampleSet> <Sample sampleID="Polystyrene_IR" derived="false"> <ParameterCategorySet> <ParameterCategory name="SampleDescription"> <ParameterSet> <Parameter name="SampleName"> <string>PolystyreneFilm</string> </Parameter> <Parameter name="SampleState"> <string>solid</string> </Parameter> </ParameterSet> </ParameterCategory> <ParameterCategory name="SubstanceDescription"> <ParameterSet> <Parameter name="SubstanceNumber"> <int>1</int> </Parameter> <Parameter name="SubstanceName"> <string>Polystyrene</string> </Parameter> </ParameterSet> </ParameterCategory> </ParameterCategorySet> </Sample> <Sample sampleID="Reference_IR" derived="false"> <ParameterCategorySet> <ParameterCategory name="SampleDescription"> <ParameterSet> <Parameter name="SampleName"> <string>air</string> </Parameter> <Parameter name="SampleState"> <string>gas</string> </Parameter> </ParameterSet> </ParameterCategory> <ParameterCategory name="SubstanceDescription"> <ParameterSet> <Parameter name="SubstanceNumber"> <int>1</int> </Parameter> <Parameter name="SubstanceName"> <string>air</string> </Parameter> </ParameterSet> </ParameterCategory> </ParameterCategorySet> </Sample> </SampleSet> <MeasurementData> <ExperimentStep name="Measurement_Polystyrene_IR"> <Author type="device"> <Name>Magna System 550</Name> </Author> <Timestamp>2002-11-06T13:03:04</Timestamp> <SamplesUsed> <SampleRef sampleID="Polystyrene_IR" role="MeasurementSample" purpose="consumed"/> </SamplesUsed> =========================================================================================== I can not understand how (without human intervention) it will be possible to decide which of the sample sampleID labels refers to a SAMPLE or BACKGROUND or REFERENCE. The labels used above are "polytyrene_ir" and "reference_ir" which can be anything the user puts there and not specific for a SAMPLE or REFERENCE. How do I decide what the sample state is for the SAMPLE when I don't know if it is the SAMPLE or REFERENCE tag that I have just read?? Does this make sense? Thanks Robert on 10/04/2006 03:10 PM Burkhard Schaefer said the following: > Robert, > >> But I note that pathlength is REQUIRED for IR. >> This can't be obtained when you do a KBr or nujol mull, surely? > > thanks for pointing this out. I have filed this as bug report #1467948 > for the IR Technique Definition. The IR Technique review team will look > into that. > > https://sourceforge.net/tracker/index.php?func=detail&aid=1467948&group_id=76803&atid=548317 > > > Burkhard > -- Prof. Robert J. Lancashire mailto:rob...@uw... Department of Chemistry Tel (876) 512 3026 University of the West Indies, Kingston 7 Fax (876) 9771835 Mona Campus, JAMAICA. http://wwwchem.uwimona.edu.jm/chrl.html |
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From: Peter M. <Pet...@re...> - 2006-04-12 14:53:21
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Robert, Can you not inspect the data to determine the resolution. This may be more accurate anyway because data from some instruments is not exactly as advertised. For example if you tell a Bruker FTIR to collect at 4 cm-1 the actual resolution is higher than that ie (3.XX). What I am saying is that the number in a resolution tag may not be entirely correct anyway. At 04:51 PM 4/10/2006 -0500, Prof. Robert John Lancashire wrote: >Burkhard, > >in conversion of JCAMP-DX files to AnIML I am concerned about >RESOLUTION as well since this is NOT required in JCAMP-DX >so will not be present in thousands of files already in existence. > >Our PE FTIR machines can be set at 1,2 or 4 cm-1 resolution so >even then I am not always sure what was the setting when the >info was recorded. > >What should go into the field in the AnIML file exported >from a JCAMP-DX file when it is given as REQUIRED? > >Another problem I have.... >I am attaching a section of a file from Anh > >============================================================== ><AnIML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" >xsi:noNamespaceSchemaLocation="animl-core.xsd" >xmlns:ds="http://www.w3.org/2000/09/xmldsig#" version="1.0"> > <SampleSet> > <Sample sampleID="Polystyrene_IR" derived="false"> > <ParameterCategorySet> > <ParameterCategory name="SampleDescription"> > <ParameterSet> > <Parameter name="SampleName"> > ><string>PolystyreneFilm</string> > </Parameter> > <Parameter > name="SampleState"> > ><string>solid</string> > </Parameter> > </ParameterSet> > </ParameterCategory> > <ParameterCategory > name="SubstanceDescription"> > <ParameterSet> > <Parameter > name="SubstanceNumber"> > <int>1</int> > </Parameter> > <Parameter > name="SubstanceName"> > ><string>Polystyrene</string> > </Parameter> > </ParameterSet> > </ParameterCategory> > </ParameterCategorySet> > </Sample> > <Sample sampleID="Reference_IR" derived="false"> > <ParameterCategorySet> > <ParameterCategory name="SampleDescription"> > <ParameterSet> > <Parameter name="SampleName"> > <string>air</string> > </Parameter> > <Parameter > name="SampleState"> > <string>gas</string> > </Parameter> > </ParameterSet> > </ParameterCategory> > <ParameterCategory > name="SubstanceDescription"> > <ParameterSet> > <Parameter > name="SubstanceNumber"> > <int>1</int> > </Parameter> > <Parameter > name="SubstanceName"> > <string>air</string> > </Parameter> > </ParameterSet> > </ParameterCategory> > </ParameterCategorySet> > </Sample> > </SampleSet> > <MeasurementData> > <ExperimentStep name="Measurement_Polystyrene_IR"> > <Author type="device"> > <Name>Magna System 550</Name> > </Author> > <Timestamp>2002-11-06T13:03:04</Timestamp> > <SamplesUsed> > <SampleRef sampleID="Polystyrene_IR" > role="MeasurementSample" purpose="consumed"/> > </SamplesUsed> >=========================================================================================== > > >I can not understand how (without human intervention) it will be possible >to decide >which of the sample sampleID labels refers to a SAMPLE or BACKGROUND or >REFERENCE. > >The labels used above are "polytyrene_ir" and "reference_ir" which can be >anything >the user puts there and not specific for a SAMPLE or REFERENCE. > >How do I decide what the sample state is for the SAMPLE when I don't know >if it >is the SAMPLE or REFERENCE tag that I have just read?? > >Does this make sense? > >Thanks >Robert > > > > > > > > >on 10/04/2006 03:10 PM Burkhard Schaefer said the following: >>Robert, >> >>>But I note that pathlength is REQUIRED for IR. >>>This can't be obtained when you do a KBr or nujol mull, surely? >>thanks for pointing this out. I have filed this as bug report #1467948 >>for the IR Technique Definition. The IR Technique review team will look >>into that. >>https://sourceforge.net/tracker/index.php?func=detail&aid=1467948&group_id=76803&atid=548317 >> >>Burkhard > > >-- >Prof. Robert J. Lancashire mailto:rob...@uw... >Department of Chemistry Tel (876) 512 3026 >University of the West Indies, Kingston 7 Fax (876) 9771835 >Mona Campus, JAMAICA. http://wwwchem.uwimona.edu.jm/chrl.html > > >------------------------------------------------------- >This SF.Net email is sponsored by xPML, a groundbreaking scripting language >that extends applications into web and mobile media. Attend the live webcast >and join the prime developer group breaking into this new coding territory! >http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 >_______________________________________________ >Animl-develop mailing list >Ani...@li... >https://lists.sourceforge.net/lists/listinfo/animl-develop ============================================================================== Peter J. Melling Ph.D. Remspec Corporation Ph. 508 248-1462 Fax. 508 248-1463 www.remspec.com ============================================================================== |
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From: Peter M. <Pet...@re...> - 2006-04-12 15:09:10
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All, We have a different problem and we are looking for pointers to anything similar that has been done. We measure time series FTIR and dispersive Raman data along with things like temperature, pressure etc on the same timescale. We also do post processing on the data to produce spectra like files with the loading v's time for those files. This can lead to a massive proliferation of files so we are considering using an AnIML like file to store the results of our handywork in one place. I would like to do this in a way that keeps as much compatibility with the existing technique AnIML schemas as possible but still meets our needs. Any comments or suggestions?? Peter Melling ============================================================================== Peter J. Melling Ph.D. Remspec Corporation Ph. 508 248-1462 Fax. 508 248-1463 www.remspec.com ============================================================================== |
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