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From: Prof. R. J. L. <rob...@uw...> - 2006-04-26 23:09:40
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Hi all, I am attaching a file that shows a sequence that I am trying to get feedback on. It is a variation of a file that Gary and Anh sent around some time ago. I noted that in the original file the Sample SampleID had 2 entries but the MeasurementData SamplesUsed only referred to the polystyrene_ID and not the reference_ID. I consider that to parse the document using StAX with a one pass through then we need to know which is the sample and which is the reference BEFORE we get down as far as <MeasurementData>. I wonder as well whether it is just a matter of adding an attribute like role to the initial Sample element as I have done in the attached file. The next things I am trying to get a handle on is whether it is going to be possible to store both the IR sample and background in the file using 2 Pages under PageSet. Once again there needs to be a way to link this info back to the SampleID etc. I have shown how this might look and it might be a replacement to the BLOCK style of a JCAMP-DX compound file? There are obviously lots of things I have forgotten but since I have not been seeing any feedback to my emails so far so I hope this might generate a response..... regards Robert |
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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...@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: 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: Peter M. <Pet...@re...> - 2006-04-19 20:18:44
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Prof. Robert John Lancashire wrote: > Hi all, > > Please excuse me while I try to come to grips with the design of > AnIML documents. I need some pointers..... sometimes the dumb questions are the smart ones. > > I have been looking at a method of parsing info out of AnIML > files using StAX (the Streaming API for XML that uses pull-based > methods). > This allows the user to read large documents with minimal overhead > which I figured was going to be an essential ingredient when we have > nD spectra or hyphenated spectral data. Nobody has responded to my plea for suggestions on the issue of nD mixed data. Does this mean we should make something up and submit it as a new technique specification. FTIR and dispersive Raman on the same reaction plus temperature and pressure data. One datapoint per minute for three days. Plus post processing including absorbance trendlines, deconvoluted peak area trend lines plus synthetic spectra and their loading v's time plots from PCA/ITTR analysis. This is a real case that we have to deal with it is not hypothetical. > > > I originally started with DOM routines (courtesy of Stuart) for reading > AnIML files for the JSpecView project but now find that there are issues > when using the Applet on a web page that seem to stop the document being > parsed even for small files. I am still not totally clear as to what > the issue > is but think it may be due to having to hold the whole file in memory > at once. > Anyway this led me to look at StAX as an alternative. (We already use > streaming methods for reading JCAMP-DX files) > > When attempting to process the document to find all the essential > variables and information needed to be able to plot the data, it seems > that the first thing that needs to be known is NOT what the SAMPLE > is but rather what the TECHNIQUE is. This then determines which > critical technique dependent parameters we need to look for. > > StAX parses through in one direction only and does not allow you to move > backwards so it would suggest that if the MEASUREMENTDATA and in > particular the EXPERIMENTSTEP came first then it would make it easier > to parse through the file to find things like NMR Frequencies etc. > Otherwise you need to store all the info somewhere and read it again. > > What this implies is that the SAMPLESET node needs to come after > the MEASUREMENTDATA node. > > This would solve the problem I have with SAMPLE info as well in that > at present there is no way of knowing which is SAMPLE/BLANK/REFERENCE > etc when processing the SAMPLESET since that information is in the > MEASUREMENTDATA under the SAMPLESUSED/SAMPLESET. It still needs > to be welll defined and I am not sure whether > role="SampleMeasurement" is a predefined STRING or free TEXT. > > Any help appreciated > > Robert > > > > > > -- Dr. Peter J. Melling PhD Remspec Corporation Charlton, MA 01508 Ph. +1 508 248-1462 Fax +1 508 248-1463 |
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From: Prof. R. J. L. <rob...@uw...> - 2006-04-19 17:42:10
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Hi all, Please excuse me while I try to come to grips with the design of AnIML documents. I need some pointers..... I have been looking at a method of parsing info out of AnIML files using StAX (the Streaming API for XML that uses pull-based methods). This allows the user to read large documents with minimal overhead which I figured was going to be an essential ingredient when we have nD spectra or hyphenated spectral data. I originally started with DOM routines (courtesy of Stuart) for reading AnIML files for the JSpecView project but now find that there are issues when using the Applet on a web page that seem to stop the document being parsed even for small files. I am still not totally clear as to what the issue is but think it may be due to having to hold the whole file in memory at once. Anyway this led me to look at StAX as an alternative. (We already use streaming methods for reading JCAMP-DX files) When attempting to process the document to find all the essential variables and information needed to be able to plot the data, it seems that the first thing that needs to be known is NOT what the SAMPLE is but rather what the TECHNIQUE is. This then determines which critical technique dependent parameters we need to look for. StAX parses through in one direction only and does not allow you to move backwards so it would suggest that if the MEASUREMENTDATA and in particular the EXPERIMENTSTEP came first then it would make it easier to parse through the file to find things like NMR Frequencies etc. Otherwise you need to store all the info somewhere and read it again. What this implies is that the SAMPLESET node needs to come after the MEASUREMENTDATA node. This would solve the problem I have with SAMPLE info as well in that at present there is no way of knowing which is SAMPLE/BLANK/REFERENCE etc when processing the SAMPLESET since that information is in the MEASUREMENTDATA under the SAMPLESUSED/SAMPLESET. It still needs to be welll defined and I am not sure whether role="SampleMeasurement" is a predefined STRING or free TEXT. Any help appreciated 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: 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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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: 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: 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 01:07:24
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Burkhard, this suggests processing the file twice or holding info in temp variables until I get down to the ExperimentStep to find the role to then try to find out which of the sampleIDs correspond to the actual sample? In my case lets say I am trying to read the file to fill in JCAMP-DX header items so that if I export as JCAMP-DX I know whether I have found the MP of the sample or the MP of the reference (for which there is NO JCAMP-DX label). That is, I've read in the sampleID's and the information given for each but don't know how to fill in the header labels until I reach the Role under ExperimentStep. It seems to me to be MUCH better to have the SampleID say exactly that this is the sample the reference or blank etc. There can't be too many alternatives to deal with. There can be another attribute that gives the info like "polystyrene_IR" but at least it is clear when processing the Sample section when I find a MP or Temp or refractive index whatever that the value is related to the SAMPLE and not the BLANK or REFERENCE. Doesn't this sound less confusing? Thanks Robert on 11/04/2006 07:16 PM Burkhard Schaefer said the following: > Robert, > >> 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? > > This is probably an error in the technique definition. I've filed a bug > for this (#1468925). > > > >> Another problem I have.... >> I am attaching a section of a file from Anh Dao > > I'm snipping out a few things for brevity. > >> >> ============================================================== >> <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"> [...] >> </Sample> >> <Sample sampleID="Reference_IR" derived="false"> [...] >> </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. > > This is determined by the Sample Role, as given in the role attribute of > the SampleRef element. Note that this happens inside the ExperimentStep, > not within the sample definition itself. > > At this point I am not sure if the list of sample roles for the IR > technique is sufficient. [This is something where the technique NDRs > will come into play.] > > >> 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. > > True. The sampleId does not contain any semantics. It is just an > identifier. > > >> 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?? > > You can have multiple SampleRef elements inside the ExperimentStep (as > declared in the Technique Definition). For example, you could have a > measured sample (role: Run Sample) and a sample used for background > subtraction (role: Background Sample). > > The names of these roles will be standardized in the Technique NDRs. > > Best regards, > 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: Burkhard S. <b_...@us...> - 2006-04-12 00:22:20
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Robert, that's odd. I haven't had problems with SourceForge mail lately. We should keep an eye on this. I've replied to your message directly and sent a copy to the list so that other people can follow as well. > By the way > Have you looked at > jspecview.sf.net > > The application will read and write JCAMP-DX/AnIML files > and the applet will import both OK but file restrictions > are limiting writing so far since the applet is not signed. > > In addition I am having some problems with DOM routines > and think I am look at StAX instead Yes, I looked at it and find it a great project. I tried it with some JCAMP data and it worked very well. Haven't tried the AnIML support yet. I agree, DOM is a pain. If you'd like something with a similar interface, I suggest JDOM. It's quite a bit easier to use (http://www.jdom.org). I haven't used StAX yet, so I can't comment on it. Best regards, Burkhard |
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From: Burkhard S. <b_...@us...> - 2006-04-12 00:16:33
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Robert, > 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? This is probably an error in the technique definition. I've filed a bug for this (#1468925). > Another problem I have.... > I am attaching a section of a file from Anh Dao I'm snipping out a few things for brevity. > > ============================================================== > <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"> [...] > </Sample> > <Sample sampleID="Reference_IR" derived="false"> [...] > </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. This is determined by the Sample Role, as given in the role attribute of the SampleRef element. Note that this happens inside the ExperimentStep, not within the sample definition itself. At this point I am not sure if the list of sample roles for the IR technique is sufficient. [This is something where the technique NDRs will come into play.] > 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. True. The sampleId does not contain any semantics. It is just an identifier. > 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?? You can have multiple SampleRef elements inside the ExperimentStep (as declared in the Technique Definition). For example, you could have a measured sample (role: Run Sample) and a sample used for background subtraction (role: Background Sample). The names of these roles will be standardized in the Technique NDRs. Best regards, Burkhard |
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From: Prof. R. J. L. <rob...@uw...> - 2006-04-11 19:58:31
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Maren it is true that you can add a $$ and a comment at the end of a header val= ue but also true that you can put in a $$ at the start of a line with a comm= ent. In the first case it is perhaps easy enough to identify what the comment referred to but not so in the second case. In fact the IR protocol had suggested that after the ##JCAMP-DX=3D label that a comment was inserted that gave the software and version that created the file. This is not always done. I note that in the Bruker "vs 6" NMR files that they have things like ##TITLE=3D ##JCAMP-DX=3D ##DATA TYPE=3D and further down may have $$ ##TITLE=3D $$ ##JCAMP-DX=3D $$ ##DATA TYPE=3D which is something I was not expecting! To try to read every JCAMP comment line and convert < and > to XML/HTML < and > is a possibility but clumsy!? Robert on 11/04/2006 09:31 AM Mar...@wa... said the following: > Hi,=20 >=20 >> Yes. There's no explicit relation between an XML comment and the=20 >> associated element. The same problem exists in JCAMP. It's hard to=20 >> determine which data item a JCAMP comment belongs to. > Is that so? I thought you could put a JCAMP comment into a line that=20 > already has a JCAMP label in it. Robert? >=20 > Mit freundlichen Gr=FC=DFen / Best regards >=20 > Maren.=20 >=20 >=20 > Dr. Maren Fiege > Product Manager > =20 > Waters GmbH > Europaallee 27, D-50226 Frechen, Germany > Tel.+49 2234 9207 - 0 Fax. +49 2234 9207-99 >=20 > http://www.waters.com/informatics=20 >=20 >=20 >=20 >=20 --=20 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...> - 2006-04-11 14:28:30
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Hi,=20 > Yes. There's no explicit relation between an XML comment and the=20 > associated element. The same problem exists in JCAMP. It's hard to=20 > determine which data item a JCAMP comment belongs to. Is that so? I thought you could put a JCAMP comment into a line that=20 already has a JCAMP label in it. Robert? Mit freundlichen Gr=FC=DFen / Best regards Maren.=20 Dr. Maren Fiege 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...> - 2006-04-10 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...> - 2006-04-10 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: 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. <bur...@bu...> - 2006-04-10 15:28:23
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Hi Stuart and Maren, >>> 2) Where should any JCAMP comments be put in the AniML file? >> At the moment, we don't have an explicit facility for comments, but >> AnIML supports the standard XML comments format ( <!-- my comment --> ). > In this case, a viewer will have to be able to read XML comments in an > AnIML file, associate them with the proper elements, and display them. > People will want to view these comments. Yes. There's no explicit relation between an XML comment and the associated element. The same problem exists in JCAMP. It's hard to determine which data item a JCAMP comment belongs to. >>> 5) If a value is required in an AnIML document but is not available in >>> the JCAMP file (or any other source file/datasystem) what should be > put >>> there? >>> Default value? No value (empty element)? >> The value cannot be left blank. That's why it's required. If the data is >> not known, you'd have to take an informed guess. > > 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. Best regards, Burkhard |
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From: <Mar...@wa...> - 2006-04-10 12:16:06
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Hi Burkhard and Stuart, > > 2) Where should any JCAMP comments be put in the AniML file? >=20 > At the moment, we don't have an explicit facility for comments, but=20 > AnIML supports the standard XML comments format ( <!-- my comment --> ). In this case, a viewer will have to be able to read XML comments in an=20 AnIML file, associate them with the proper elements, and display them.=20 People will want to view these comments. =20 > > 4) If a piece of header information has no obvious place to go in the=20 > > AnIML file where should it be put? (or does this suggest a change in=20 > > the ATID is needed?) >=20 > Four possibilities: > - create an Extension > - file a bug report with the appropriate Technique team ;-) > - use an XML comment > - ignore the data We have to revisit the ATIDs anyway. While doing that, we can make sure=20 the JCAMP header info gets a place to put it. =20 > > 5) If a value is required in an AnIML document but is not available in = > > the JCAMP file (or any other source file/datasystem) what should be=20 put=20 > > there? > > Default value? No value (empty element)? >=20 > The value cannot be left blank. That's why it's required. If the data is = > not known, you'd have to take an informed guess. Unfortunately, informed guesses are not 21 CFR 11 compliant (no accurate=20 copy of records). It is the task of the technique definition groups to=20 make sure the required AnIML elements can be filled. Mit freundlichen Gr=FC=DFen / Best regards Maren.=20 Dr. Maren Fiege 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: Burkhard S. <bur...@bu...> - 2006-03-26 21:35:41
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Stuart, > 1) How does any converter appropriately identify that it did the > conversion? Do we need a "Conversion" Action in the AuditTrail? as it stands, the most appropriate Action to use would be "created", since (by performing the conversion) the converter creates the entries in the AnIML document. > 2) Where should any JCAMP comments be put in the AniML file? At the moment, we don't have an explicit facility for comments, but AnIML supports the standard XML comments format ( <!-- my comment --> ). > 3) Instrument Vendor specific parameters should go where? (until the > vendors add their module) You'd create and reference an AnIML Technique Extension document. If the parameters are known before the measurement (instrument settings, instrument info, ...), the data is stored as Parameters within the ExperimentStep. If the data was actually measured, it goes into Page Parameters. > 4) If a piece of header information has no obvious place to go in the > AnIML file where should it be put? (or does this suggest a change in > the ATID is needed?) Four possibilities: - create an Extension - file a bug report with the appropriate Technique team ;-) - use an XML comment - ignore the data > 5) If a value is required in an AnIML document but is not available in > the JCAMP file (or any other source file/datasystem) what should be put > there? > Default value? No value (empty element)? The value cannot be left blank. That's why it's required. If the data is not known, you'd have to take an informed guess. > 6) To go along with 5)...if a required field is defined with enum list > what should be chosen if there is no data available? > Add an "Unknown" enum value to each such list? Again, you need to take an informed guess. Note: Data that is typically difficult to obtain will not be made a required entry in the Standard Technique Definitions. Best regards, Burkhard |
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From: Chalk, S. <sc...@un...> - 2006-03-21 00:47:33
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At last weeks PittCon working group meeting, suggestions were made regarding the converter and I have addressed those in an update today. You will find example files for download on the converter page (fad.coas.unf.edu/animl/jcampconversion.php). These are 2D data files only. In addition, I have increased the upload file size and changed the error message (sorry Maren). Through putting this converter together I have come across some issues that need to be thought about on this list. I reported some of them at the meeting last week but have thought of some more so I have summarized them below. 1) How does any converter appropriately identify that it did the conversion? Do we need a "Conversion" Action in the AuditTrail? 2) Where should any JCAMP comments be put in the AniML file? 3) Instrument Vendor specific parameters should go where? (until the vendors add their module) 4) If a piece of header information has no obvious place to go in the AnIML file where should it be put? (or does this suggest a change in the ATID is needed?) 5) If a value is required in an AnIML document but is not available in the JCAMP file (or any other source file/datasystem) what should be put there? Default value? No value (empty element)? 6) To go along with 5)...if a required field is defined with enum list what should be chosen if there is no data available? Add an "Unknown" enum value to each such list? Sorry for so much detail, but I got stimulated at PittCon ;) Stuart Chalk |
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From: Chalk, S. <sc...@un...> - 2006-02-23 18:26:11
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AnIML Developers This is to announce that I have put up a page that performs JCAMP-DX to AnIML conversion online. This is an alpha release and thus may have some bugs but please try it out and send me feedback on its functionality. http://fad.coas.unf.edu/animl/jcampconversion.php Stuart Chalk, Ph.D. Associate Professor of Chemistry Department of Chemistry and Physics University of North Florida P: 904-620-1938 F: 904-620-1989 E: sc...@un... |
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From: David M. <d_m...@ac...> - 2005-12-15 22:01:27
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The minutes of the last several meetings of the AnIML working group have been posted to the AnIML web site. See the "Meetings" link at http://animl.sf.net <http://animl.sf.net/> . Included are: * December 2, 2005 Virtual Meeting * November 14, 2005 Business Meeting at EAS * November 13, 2005 Working Group meeting at EAS * October 28, 2005 Virtual Meeting * October 14, 2005 Virtual Meeting Sorry for the delay. Dave ********************************* David Martinsen American Chemical Society 1155 16th St. NW Washington, DC 20036 d_m...@ac... |
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