# Semantic Metadata Annotation Services in the Biomedical Domain--A Literature Review
## 5 Discussion  
This review has provided an overview of semantic metadata annotation services in the biomedical field. For this purpose, we reviewed over 200 research articles retrieved via PubMed and Google Scholar. Most of the articles, although meeting our search criteria, had to be excluded from the review because they were not relevant. The criterion for inclusion of a publication in this review was the description and provision of a service for semantic metadata annotation. Thus, only articles describing a standalone service for linking metadata elements to semantic concepts were considered. A number of services consist of components that provide supporting services, such as offering semantic concepts for enrichment/annotation or linking a text snippet within a data object to the corresponding semantic code (see Section 3). Such supporting services play an important role in the development of a semantic metadata annotation service, as formulated in Requirements 3 (FAIR terminologies), 4 (terminology search) and 5 (annotation suggestion). However, named entity recognition methods for text mining in particular are an extensive topic, and reviewing those components is beyond the scope of this review. Furthermore, there are ontology-dependent web-services that integrate the display of semantic concepts and their associations with text fragments (e.g., [29; 51]). They can be seen as a complement to ontology/terminology services rather than standalone services because they only accept unstructured text as input and do not involve the human in the loop. Based on these criteria, ten relevant articles/software systems were identified and summarized in this work. In addition, we analyzed the extent to which these systems meet the seven basic requirements we have defined in the context of the research data infrastructure project NFDI4 Health. Annotation services are needed to support researchers in using standard data formats and semantic annotations towards external terminologies. Annotation suggestions can support the annotation process in this regard. Furthermore, such services should be openly accessible and should provide access to FAIR terminologies for annotation. Finally, in order to meet the needs of different research areas and to integrate the services into already established methods and workflows, a range of formats and terminologies should be supported. No tool met all the requirements completely. The annotation services Rightfield, CEDAR Workbench, OntoMaton, SAP and Metadata-Enricher provide interfaces to ontology portals (NCBO Bioprotal or OLS) and have in such a way a broad coverage. However, they do not seem to have interfaces for additional terminology integration. Only Rightfield and D2 Refine provide the opportunity to upload local files, whereby D2 Refine limits the upload to CTS2-compliant terminologies. ODMedit, Swate, eleMAP and Prototype Wiktorin are tailored to specific use cases and also do not seem to have interfaces for additional terminology integration. However, the Swate terminologies could be adapted by Swate administrators. Rightfield and OntoMaton are designed for Microsoft Excel and Google Spreadsheets, respectively, and are not capable of handling other formats currently. Several tools offer annotation suggestions: either straightforwardly by providing similar annotations or by performing string matching (ODMedit, eleMAP and Prototype Wiktorin) or in a more complex way by using a concept recognition tool (SAP). SAP and eleMAP appear to be promising in terms of annotation suggestions, although neither has released code yet and neither is publicly available. ODMedit's approach to annotation suggestions allows for consistent semantic annotation based on UMLS concepts already used in other MDM-portal questionnaires. Whereas this is a great advantage for already existing concepts, it makes the annotation of new concepts cumbersome. Another service under current development is Snap2 Snomed [52].