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I am involved in a project where we need a solution for manual #annotation of the contents of patient medical records stored in an #XML format.
Which #tool can help do this, or does such a tool even exist?
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How can I manually annotate data in XML?

I am involved in a project where we need a solution for manually annotating the contents of patient medical records stored in an XML format. We need a tool to show the contents of the fields of the...
Data Science Stack Exchange
#annotation #xml #tool
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Alan Sill
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Alan Sill
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If you have a fixed format for the patient records, you can write a DFDL description of that format and then a description of the fields you want to add. Various tools including Daffodil (open source) or commercial (e.g., from IBM) can perform transformation on the records to go from the old to the new formats. Schemas for your records may already exist (e.g., if they are HIPAA-5010 already): see github.com/orgs/DFDLSchemas/re… and there is a tutorial on DFDL at ogf.org/dfdl

DFDL Schemas for Commercial and Scientific Data Formats

DFDL Schemas for Commercial and Scientific Data Formats has 28 repositories available. Follow their code on GitHub.
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@AlanSill I am not completely sure what fixed format means here. It is in a well-defined XML format called FNUX: medcom.dk/medcom-in-english/st…, but it is only used in a Danish context. It is not fixed in the sense that many fields are optional and there can be arbitrary numbers of certain fields.
They are in a process of modernising data formats to HL7 FHIR, which I know almost nothing about yet. I don't think I would be able to get data in that format yet.

Standards - MedCom

MedCom
@Alan Sill
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Alan Sill
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Alan Sill
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You're in luck! Medcom's software is based on HL7 standards for which DFDL schema and tools already exist. IBM has tools to do this as described at ibm.com/docs/en/integration-bu… and ot4i.github.io/dfdl-hl7-tutori… and Medcom software seems already set up to handle metadata. By "annotation" I was assuming you meant "adding more fields to the record" which is why I suggested transformation, but you might be able to use these existing tools to handle the annotation you need. Reach out if you need help.

IBM Integration Bus V10 Tutorial

ot4i.github.io
This entry was edited (2 years ago)
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Alan Sill
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Alan Sill
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This looks useful if you want to go the Medcom route: github.com/orgs/medcomdk/repos…
If it were me, I'd start by talking to them about what you want to do. We can also handle new tools and schema development if needed (see nsfcac.org) if there's something you want to do that isn't handled by existing (e.g., Medcom or IBM) tools. Let us know if you need help.

MedCom

MedCom has 34 repositories available. Follow their code on GitHub.
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@AlanSill when you suggest NSFCAC, I get the impression you mean in a US context? I work at a university in Denmark, so I am not sure this would apply to me?
@Alan Sill
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Alan Sill
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Alan Sill
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Probably not. I can try to find you an equivalent center in Europe to help. Would Switzerland be okay?
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@AlanSill I guess it's always worth investigating. I don't know if the caveat that Switzerland is not in the EU might play a role.
I really appreciate your suggestions.
@Alan Sill
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Alan Sill
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Alan Sill
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I know an expert in DFDL at IBM in the UK -- also not in the EU any more! Too many boundaries these days. Will DM you some contact info so you can ask them about what you are doing. (Please be sure to provide the background.)
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@AlanSill sounds really promising. Are you referring to the HL7 FHIR format Medcom say they are working on? Because I only have the data in their older FNUX format and AFAIK I cannot obtain it in any other format.
By annotation I mean that for each field in the FNUX file (in principle but in practice only some fields), I need to add a field associated with it, holding a comment or predefined code.
@Alan Sill
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@AlanSill each such associated field enables a physician to state: "the contents of this field are important to a diagnosis this patient has", "the contents of this field are unrelated to the diagnosis of interest", or something along those lines.
On top of that, I will need to provide a GUI to allow physician annotators to read the contents of the FNUX file and enter the annotations alongside.
@Alan Sill
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Alan Sill
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Alan Sill
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Most of the information on FNUX I can find on the web seems to come from Denmark and to be several years old. These links seem to have useful information: isfteh.org/files/media/Medcom.… and researchgate.net/publication/2… but just confirm the existence and usefulness of FNUX. I am not an expert in these formats, but any time you are looking to add fields to a data format, you will either need to find an existing capability w/the standard for that field or extend the format using tools like mentioned.
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@AlanSill I also have the impression from MedCom that the existing FNUX format is not being developed any further and that it is going to be replaced by more modern standards.
I am not hell-bent on the FNUX format if I can just convert it to something else useful for my annotation end goal.
My main goal here is to find a useful annotation tool and as long as I can find a way to coerce the data from FNUX into it, that will suffice.
@Alan Sill

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