## 4 Discussion & Conclusions
Similarly, Planteome database [27] provides gene annotations and phenotypes with the help of reference ontologies such as PO, TO, GO and CheBI. Planteome is a user-friendly tool to query traits of interest, germplasm, and putative candidate genes. However, it lacks QTLs, genetic markers and links to publicly available databases such as Ensembl Plants. Therefore, our Linked Data platform is a unique resource for _Solanaceae_ species that provides access to available knowledge about genome annotations in public databases and scientific literature. pbg-ld currently contains the gene models and the genetic markers based GFF files of the reference tomato genome (_S. lycopersicum_), wild tomato (_S. pennellii_), and the reference potato genome(_S. tuberosum_). However, other than these genomes, the SGN database, for instance also includes GFF files from other _Solanaceae_ and closely related genomes species, such as reference genome of pepper (_Capsicum annuum_) [82], eggplant (_Solanum melongena_ L.) [83] and so forth. Converting these GFF files to RDF graphs and adding them to the pbg-ld would improve analyses based on comparative genomics. Nevertheless, a big challenge in doing this type of analysis based on knowledge graphs is to have the mappings of biological entities (genes, proteins, etc.) across multiple species. There is a chance of having different identifiers in two related species, for example, the genomes of the reference sequence potato _S. tuberosum_ and wild type species _M6_ have both been sequenced, however, both use different sets of identifiers and the mapping of genes between these genotypes is not available. However, having the data about cross references in these genes for both the genomes can give us better insights into underpinning certain gene functions with comparative studies. To conclude, pbg-ld is an integrated resource for _Solanaceae_ species that provides access to available knowledge about genome annotations in public databases and scientific literature. This resource aids in the identification of candidate genes for complex traits using available knowledge in the databases and literature. Conceptualization: G.S., R.F., A.K., R.G.F.V. ; methodology: G.S., A.K., R.F. ; software: [PERSON], M.B., G.S., C.M.-O. ; validation: [PERSON], C.W.B.B., Y.M.T., A.G.B. ; formal analysis: [PERSON], A.K. ; investigation: [PERSON], A.K., C.W.B.B. ; resources: A.K., M.B., G.S. ; data curation: [PERSON], G.S., M.B. ; writing-original draft preparation: [PERSON], A.K. ; writing-review and editing: [PERSON], A.K., [PERSON], C.W.B.B., R.F. ; visualization: [PERSON], A.K., M.B. ; supervision: [PERSON], C.W.B.B., [PERSON], R.F. ; project administration: R.G.F.V., A.K., G.S., R.F. ; funding acquisition: R.G.F.V., R.F. All authors have read and agreed to the published version of the manuscript. This work was supported by the Netherlands Organisation for Scientific Research (NWO) via the Netherlands eScience Center (grant number: 27014204). We thank [PERSON] for stimulating discussions and guidance. This article is based on the results of one of the chapters of the Ph.D thesis of the first author [PERSON] entitled \"Genomics data integration for knowledge discovery using genome annotations from molecular databases and scientific literature\" delivered at Wageningen University [84]. This work was carried out on the Dutch national e-infrastructure with the support of SURF Foundation. The authors declare no conflict of interest. * [PERSON] et al. (2014) [PERSON]; [PERSON]; [PERSON]; [PERSON] [PERSON]; [PERSON] [PERSON] Inferring the gene network underlying the branching of tomato inflorescence. _PLoS ONE_**2014**, 9, e89689. [CrossRef] [PubMed]
* [PERSON] et al. (2012) [PERSON] [PERSON]; [PERSON]; [PERSON]; [PERSON] Quantitative Trait Locus (QTL) meta-analysis and comparative genomics for candidate gene prediction in perennial ryegrass (_Lolium perenne L._). _BMC Genet._**2012**, _13_, 101. [CrossRef] [PubMed]
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