#  1 Introduction

This deliverable is the initial version of the data management plan. In this
document, the data generated by the KConnect project is identified and the
current status of the data management, archiving, preservation and licensing
plans are given. In particular, this initial analysis of the data indicates
where further efforts are required to clearly specify these aspects of the
data management plan. The final version of the data management plan is D6.3
due in July 2016.

Each section of this deliverable describes a data resource identified in the
KConnect project. The format followed in each section corresponds to the
structure proposed in the European Commission Guidelines on Data Management in
Horizon 2020 [1].

In summary, Sections 2 to 5 deal with data for which no privacy issues exist
(knowledge base, machine translation training data, and annotations and
indices), while Sections 6 to 9 deal with data in which care needs to be taken
to ensure that privacy is preserved (search logs and medical records).

#  2 Knowledge Base

**2.1 Name**

Knowledge Base

##  2.2 Description

The knowledge base is a warehouse of semantically integrated data sets
published originally by third parties. It includes information on drugs, drug
targets, drug interactions, diseases, symptoms, adverse events, anatomies and
imaging modalities. In addition to the data sets it includes link sets that
map data between the different data sets and/or provide semantic
relationships. The data is available as RDF and is loaded into a GraphDB [2]
repository.

Original data sets:

  * Drugbank 

  

  * UMLS 

  

  * RadLex 

  

  * DBPedia (medical subset) 

  

  * GeoNames 

  

##  2.3 Standards and metadata

The data is available in different RDF formats: RDF-XML, NTriple, Turtle,
TriG, TriX and RDF-JSON. It can be queried via SPARQL and the KB exposes the
OpenRDF REST API.

**2.4 Data sharing conditions**

Data sharing varies according to the sharing conditions associated with the
original data sets.

##  2.5 Archiving and preservation

Archiving and preservation varies according to the Archiving and preservation
arrangements associated with the original data sets. Ontotext stores backups
of the data sets converted to RDF and the corresponding link sets on its
servers.

**2.6 Licensing information**

Licensing varies according to the licensing of the original data sets.

#  3 Summary Translation Test Data

**3.1 Name**

Khresmoi Summary Translation Test Data 1.1

##  3.2 Description

This dataset contains data for development and testing of machine translation
of sentences from summaries of medical articles between Czech, English,
French, and German. The original sentences are sampled from summaries of
English medical documents crawled from the web in 2012 and identified to be
relevant to 50 medical topics.

The original sentences in English were randomly selected from automatically
generated summaries of documents from the CLEF 2013 eHealth Task 3 collection
[1] which were found to be relevant to 50 test topics provided for the same
task. Out-of-domain and ungrammatical sentences were manually removed. The
sentences are provided with information on document ID and topic ID. The topic
descriptions are provided as well. The sentences were translated by medical
experts into Czech, French, and German and reviewed. The data sets can be
used, for example, for the development and testing of machine translation in
the medical domain.

##  3.3 Standards and metadata

The data is provided in two formats: plain text and SGML. They are split
according to the section (dev/test) and language (CS – Czech, DE - German, FR
- French, EN – English). All the files use the UTF-8 encoding. The plain text
files contain one sentence per line and translations are identified by line
numbers. The SGML format suits the NIST MT scoring tool. Topic description
format is based on XML, each topic description (<query>) contains the
following tags:  
  
<table>  
<tr>  
<th>

**Tag**

</th>  
<th>

**Description**

</th> </tr>  
<tr>  
<td>

<id>

</td>  
<td>

topic ID

</td> </tr>  
<tr>  
<td>

<discharge_summary>

</td>  
<td>

reference to discharge summary

</td> </tr>  
<tr>  
<td>

<title>

</td>  
<td>

text of the query

</td> </tr>  
<tr>  
<td>

<desc>

</td>  
<td>

longer description of what the query means

</td> </tr>  
<tr>  
<td>

<narr>

</td>  
<td>

expected content of the relevant documents

</td> </tr>  
<tr>  
<td>

<profile>

</td>  
<td>

profile of the user

</td> </tr> </table>

**3.4 Data sharing conditions**

Access to this data set is widely open under the license specified below.

##  3.5 Archiving and preservation

The data set is distributed by the LINDAT/Clarin project of the Ministry of
Education, Youth and Sports of the Czech Republic and is available here:
_http://hdl.handle.net/11858/00-097C-0000-0023-866E-1_

##  3.6 Licensing information

The data set is made available under the terms of the Creative Commons
Attribution-Noncommercial (CC-BY-NC) license, version 3.0 unported. A full
description and explanation of the licensing terms is available here:
_http://creativecommons.org/licenses/by-nc/3.0/_

#  4 Query Translation Test Data

**4.1 Name**

Khresmoi Query Translation Test Data 1.0

##  4.2 Description

This data sets contains data for development and testing of machine
translation of medical queries between Czech, English, French, and German. The
queries come from general public and medical experts.

The original queries in English were randomly selected from real user query
logs provided by Health on the Net foundation (750 queries by general public)
and from the Trip database query log (758 queries by medical professionals)
and translated to Czech, German, and French by medical experts. The test sets
can be used, for example, for the development and testing of machine
translation of search queries in the medical domain.

##  4.3 Standards and metadata

The data is split into 8 files, according to the section (dev/test) and
language (CS - Czech, DE - German, FR - French, EN – English). The files are
in plain text using the UTF-8 encoding. Each line contains a single query.
Translations are identified by line numbers.

**4.4 Data sharing conditions**

Access to this data set is widely open under the license specified below.

##  4.5 Archiving and preservation

The data set is distributed by the LINDAT/Clarin project of the Ministry of
Education, Youth and Sports of the Czech Republic and is available here:
_http://hdl.handle.net/11858/00-097C-0000-0022-D9BF-5_

##  4.6 Licensing information

The data set is made available under the terms of the Creative Commons
Attribution-Noncommercial (CC-BY-NC) license, version 3.0 unported. A full
description and explanation of the licensing terms is available here:
_http://creativecommons.org/licenses/by-nc/3.0/_

#  5 Annotated Text Data

**5.1 Name**

Text and annotation indices

##  5.2 Description

The dataset comprises texts annotated and indexed by the KConnect semantic
annotation pipeline, in order to create a searchable index with links to the
KConnect knowledge base.

There are several datasets, each held by the KConnect partner that is
responsible for the underlying texts. In the next version of this deliverable,
these datasets will be individually identified and described, as the plan for
the progress of the KConnect work does not allow this to be done at this
stage.

##  5.3 Standards and metadata

Texts are annotated using a Text Encoding Initiative (TEI) compliant
framework, GATE [3, 4], to create documents encoded with UTF-8, in GATE XML
format.

Annotations are linked to the knowledge base using URIs, and are searchable
using SPARQL

**5.4 Data sharing conditions**

Data sharing varies according to the sharing conditions associated with the
underlying text collection.

##  5.5 Archiving and preservation

Archiving and preservation varies according to the archiving and preservation
arrangements associated with the underlying text collection.

**5.6 Licensing information**

Licensing varies according to the licensing of the underlying text collection.

#  6 HON Search Logs

**6.1 Name**

HONSearchLogs

##  6.2 Description

Search Engine Logs provided by the Health On the Net Foundation (HON). This
data set contains the query logs collected from various search engines
maintained by HON. The search engine logs are collected over a period of over
3 years (since November 2011) and are continuing to be collected.

The search engine logs contain following information:

  * query term 

  

  * users’ IP address – which enables determining the geographical distribution of the search 

  

  * exact date and time of the query 

  

  * language 

  

  * information on the search engine used to perform the search (honSearch, honSelect, …)  information on the link followed 

  

##  6.3 Standards and metadata

The search logs will be provided in the XML format, for which the metadata
will be provided. An illustration of the format draft is given in the Figure
1.

**Figure**

**1**

**. Sea**

**rch Log format draft**

##  6.4 Data sharing conditions

This data set is provided by HON for the project partners. This data can be
used for analysis of users’ behaviour linked to the search engine usage.

With the goal of preservation of the users' personal data, the original
content of the search logs is modified by HON. This modification consists of
masking the part of the users' IP address, however keeping the parts of the IP
which would enable the analysis of the global users' whereabouts. In the above
shown format draft the alternations of the original query logs are marked with
“*”.

##  6.5 Archiving and preservation

The original search logs are archived and kept on HON premises for the period
of 5 years. These archives consist of the original, non-treated search logs.
Investigation is underway for a possibility for longerterm preservation of the
anonymised logs.

##  6.6 Licensing information

The HONSearchLogs will be made available on demand by the partners. The data
are distributed under the terms of the Creative Commons Attribution-ShareAlike
(CC-BY-SA), version 3.0 unported. A full description and explanation of the
licensing terms is available here:

_https://creativecommons.org/licenses/by-sa/3.0/_

#  7 TRIP Database Search Logs

**7.1 Name**

Trip Database search logs

##  7.2 Description

As users interact with the Trip Database  ( _https://www.tripdatabase.com_ )
the site captures the user’s activity. It records search terms and articles
viewed. In addition this data is linked to the user so that information about
profession, geography, professional interests etc. can be considered. This may
be useful in helping understand the search process, important documents,
linked concepts etc.

There is considerable data going back multiple years and is constantly being
collected.

**7.3 Standards and metadata**

There are no official standards.

##  7.4 Data sharing conditions

The data can be shared with the KConnect consortia with prior permission.
Outside of KConnect the sharing of the data will be by negotiation.

Currently the data needs to be requested and downloaded by the Trip Database
but an API is being considered.

##  7.5 Archiving and preservation

The data is stored on the Trip servers and these are backed up and saved on a
daily basis. The production of the search logs is independent of the KConnect
project and is increasingly core to the development of the Trip Database. As
such the costs are seen as core to Trip.

**7.6 Licensing information**

There is currently no formal licensing information.

#  8 KCL Patient Records

**8.1 Name**

The South London and Maudsley NHS Foundation Trust (SLAM) Hospital Records

##  8.2 Description

The South London and Maudsley NHS Foundation Trust (SLAM) is the largest
provider of mental health services in Europe. The hospital electronic health
record (EHR), implemented in 2007, contains records for 250,000 patients in a
mixture of structured and over 18 million free text fields.

At the NIHR Biomedical Research Centre for Mental Health and Unit for Dementia
at the Institute of Psychiatry, Psychology and Neuroscience (IOPPN), King’s
College London we have developed the Clinical Record Interactive Search
application (CRIS,  _http://www.slam.nhs.uk/about/corefacilities/cris_ )  ,
which allows research use of the pseudonymised mental health electronic
records data (with ethics approval since 2008).

##  8.3 Standards and metadata

Through this model we will be able to provide access to a regular snapshot of
the complete set of pseudonymised records in XHTML format.

**8.4 Data sharing conditions**

Records can be accessed by collaborators either onsite or through a remote
secure connection.

**8.5 Archiving and preservation**

The record system is maintained by hospital IT services.

**8.6 Licensing information**

Data access is governed through a patient led oversight committee.

#  9 Qulturum Patient Records

**9.1 Name**

Region Jönköping County Patient Records

##  9.2 Description

Region Jönköping County (RJC) provides test data consisting of 50 fictitious
patient records with the same data structure and content as a real patient
record, in Region Jönköping County’s electronic health records system
(Cosmic), would have.

RJC will also provide real patient records if needed. In order to do so, the
anonymisation process must be secured. The number of patient records that will
be provided depends on how much data is needed in order to develop and test
the KConnect solution. The first step of using test data instead of real
patient records is necessary in order to secure that the tool is correctly
adapted and implemented before real EHR content is used.

##  9.3 Standards and metadata

The use case(s) decided on will determine how data will be manipulated, e.g.
addition of metadata/annotations.

**9.4 Data sharing conditions**

Records data be created, stored/archived, accessed, used and kept secure by
Jönköping staff on site.

**9.5 Archiving and preservation**

An archiving and preservation plan is under development.

**9.6 Licensing information**

There is currently no formal licensing information.

#  10 Conclusion

This deliverable presents the initial version of the Data Management Plan for
the KConnect project. It identifies data that is being collected in the
KConnect project and allows missing information to be identified. An updated
version of the deliverable that will include the information currently not
available will be released as D6.3 in July 2016\.