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BMC Med Inform Decis Mak. 2016 Aug 2;16:101. doi: 10.1186/s12911-016-0333-0.

Searching for rare diseases in PubMed: a blind comparison of Orphanet expert query and query based on terminological knowledge.

Author information

1
Department of Biomedical Informatics, Rouen University Hospital, TIBS, LITIS EA 4108, Rouen University, 76031, Rouen Cedex, France. nicolas.griffon@chu-rouen.fr.
2
INSERM, U1142, LIMICS, 75006, Paris, France; Sorbonne Universités, UPMC Univ Paris 06 UMR_S 1142, LIMICS, 75006, Paris, France; Univ Paris 13, Sorbonne Paris Cité, LIMICS (UMR_S 1142), 93430, Villetaneuse, France. nicolas.griffon@chu-rouen.fr.
3
Department of Biomedical Informatics, Rouen University Hospital, TIBS, LITIS EA 4108, Rouen University, 76031, Rouen Cedex, France.
4
Department of Family Practice, Rouen University, Rouen, France.
5
INSERM, U1142, LIMICS, 75006, Paris, France; Sorbonne Universités, UPMC Univ Paris 06 UMR_S 1142, LIMICS, 75006, Paris, France; Univ Paris 13, Sorbonne Paris Cité, LIMICS (UMR_S 1142), 93430, Villetaneuse, France.
6
Service de Médecine Fœtale, Hôpital Trousseau - Hôpitaux Universitaires de l'Est Parisien (APHP), Université Pierre et Marie Curie, Paris, France.
7
Department of Occupational Medicine, Rouen University Hospital, Rouen, France.

Abstract

BACKGROUND:

Despite international initiatives like Orphanet, it remains difficult to find up-to-date information about rare diseases. The aim of this study is to propose an exhaustive set of queries for PubMed based on terminological knowledge and to evaluate it versus the queries based on expertise provided by the most frequently used resource in Europe: Orphanet.

METHODS:

Four rare disease terminologies (MeSH, OMIM, HPO and HRDO) were manually mapped to each other permitting the automatic creation of expended terminological queries for rare diseases. For 30 rare diseases, 30 citations retrieved by Orphanet expert query and/or query based on terminological knowledge were assessed for relevance by two independent reviewers unaware of the query's origin. An adjudication procedure was used to resolve any discrepancy. Precision, relative recall and F-measure were all computed.

RESULTS:

For each Orphanet rare disease (n = 8982), there was a corresponding terminological query, in contrast with only 2284 queries provided by Orphanet. Only 553 citations were evaluated due to queries with 0 or only a few hits. There were no significant differences between the Orpha query and terminological query in terms of precision, respectively 0.61 vs 0.52 (p = 0.13). Nevertheless, terminological queries retrieved more citations more often than Orpha queries (0.57 vs. 0.33; p = 0.01). Interestingly, Orpha queries seemed to retrieve older citations than terminological queries (p < 0.0001).

CONCLUSION:

The terminological queries proposed in this study are now currently available for all rare diseases. They may be a useful tool for both precision or recall oriented literature search.

KEYWORDS:

Bibliography as topic; PubMed; Rare diseases; Terminology as topic

PMID:
27484923
PMCID:
PMC4970261
DOI:
10.1186/s12911-016-0333-0
[Indexed for MEDLINE]
Free PMC Article

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