Literature-based discovery of diabetes

reactive oxygen species (ROS) atomic number 18 known mediators of cellular damage in multiple diseases including diabetic complications. despite its importance, no general database is authorizedly available for the genes associated with ROS. Methods We arrange ROS- and diabetes- cogitate gets (genes/proteins) pile up from the biomedical writings through a school text archeological site technology. A web-based literary productions mining tool, SciMiner, was applied to 54 biomedical papers indexed with diabetes and ROS by PubMed to commit relevant invests.Over- represented gets in the ROS-diabetes publications were obtained through comparisons against willy-nilly selected literature. The face levels of nine genes, selected from the top ranked ROS-diabetes set, were calculated in the dorsal understructure ganglia (DRG) of diabetic and non-diabetic DBA/2J mice in severalise to evaluate the biological relevancy of literature- derived designs in the pathogenesis of diabetic neuropathy. Results SciMiner place 1,026 ROS- and diabetes- cerebrate targets from the 54 biomedical papers (http//Jdrf. eurology. med. umich. edu/ROSDiabetes/ webcite). Fifty- ternion targets were importantly over-represented in the ROS-diabetes literature ompargond to helter-skelter selected literature. These over-represented targets included well-known members of the oxidative render response including catalase, the NADPH oxidase family, and the superoxide anion anion dismutase family of proteins. Eight of the nine selected genes bring outed signifi kittyt differential feeling betwixt diabetic and non-diabetic mice.For six genes, the direction of comportion cargonen in diabetes reduplicateed raise oxidative tense up in the DRG. Conclusions Literature mining compiled ROS-diabetes related targets from the biomedical literature and led us to evaluate the biological relevance of selected targets in the athogenesis of diabetic neuropathy. Diabetes is a metabolic d isease in which the corpse does non produce or properly respond to insulin, a endocrine required to convert carbohydrates into energy for daily flavor. According to the Ameri squeeze out Diabetes Association, 23. one million million children and adults, approximately 7. 8% of the population in the United States, obtain diabetes 1. The apostrophize of diabetes in 2007 was estimated to be $174 billion 1. The micro- and macro-vascular complications of diabetes are the most common causes of nephritic tailure, blindness and amputations leading to operative morta y, morbidity poor quality of life however, incomplete understanding of the causes of diabetic complications hinders the development of mechanism-based therapies.In vivo and in vitro experiments implicate a number of enzymatic and non-enzymatic metabolic pathways in the initiation and progression of diabetic complications 2 including (1) increase polyol pathway activity leading to sorbitol and fructose accumulation, NAD(P )-redox imbalances and changes in designate transduction (2) non- enzymatic glycation of proteins yielding advanced glycation end-products (AGES) (3) ctivation of protein kinase C (PKC), initiating a cascade of intracellular pains responses and (4) change magnitude hexosamine pathway flux 2,3.Only recently has a liaison among these pathways been established that erects a unified mechanism of tissue damage. Each of these pathways at one time and indirectly leads to overproduction of thermolabile oxygen species (ROS) 23. ROS are highly reactive ions or small molecules including oxygen ions, free radicals and peroxides, formed as cancel byproducts of cellular energy metabolic bidding. ROS are implicated in multiple cellular pathways such(prenominal) as mitogen-activated protein kinase MAPK) sign of the zodiac, c-Jun amino-terminal kinase ONK), cell proliferation and apoptosis 4-6.Due to the highly reactive properties of ROS, inordinate ROS whitethorn cause significant damage to proteins, DNA, RNA and lipids. All cells express enzymes capable of neutralizing ROS. In addition to the maintenance of antioxidant systems such as glutathione and thioredoxins, uncreated sensory neurons express deuce main detoxifying enzymes superoxide dismutase (SOD) 7 and catalase 8. SOD converts superoxide (02-) to H202, which is reduced to H20 by glutathione and catalase 8.SODI is the main form of SOD in the cytoplasm SOD2 is located deep down the itochondria. In neurons, SODI activity represents approximately 90% of fare SOD activity and SOD2 approximately 10% 9. Under diabetic conditions, this protective(p) mechanism is overwhelmed due to the substantial increase in ROS, leading to cellular damage and dysfunction 10. The idea that increased ROS and oxidative stress sum to the pathogenesis of diabetic complications has led scientists to investigate different oxidative stress pathways 7,11.Inhibition of ROS or maintenance of euglycemia restores metabolic and vascular imb alances and blocks twain the initiation and progression of omplications 1 2,13. Despite the significant implications and extensive research into the role of ROS in diabetes, no comprehensive database regarding ROS-related genes or proteins is currently available. In the present study, a comprehensive incline of ROS- and diabetes-related targets (genes/proteins) was compiled from the biomedical literature through text mining technology.SciMiner, a web-based literature mining tool 14, was apply to retrieve and dish documents and aim targets from the text. SciMiner provides a convenient web-based platform for target- naming at bottom the biomedical iterature, similar to other tools including EBIMed 1 5, ALI BABA 16, and Polysearch 1 7 however, SciMiner is rum in that it searches tull text documents, suppo free-text PubMed query style, and allows the comparison of target lists from multiple queries.The ROS-diabetes targets pile up by SciMiner were further tested against randomly selected non-ROS-diabetes literature to identify targets that are importantly over- represented in the ROS-diabetes literature. available enrichment analyses were performed on these targets to identify importantly over-represented biological unctions in terms of Gene Ontology (GO) terms and pathways. In order to confirm the biological relevance of the over-represented ROS-diabetes targets, the gene convention levels of nine selected targets were measured in dorsal root ganglia (DRG) from mice with and without diabetes.DRG contain primary sensory neurons that pass along in organisation from the periphery to the central nervous system (CNS) Unlike the CNS, DRG are not protected by a blood-nerve barrier, and are consequently unsafe to metabolic and toxic injury 19. We hypothesize that differential facial gesture of place targets in DRG would confirm heir involvement in the pathogenesis of diabetic neuropathy. be ROS-diabetes literature To retrieve the list of biomedical literat ure associated with ROS and diabetes, PubMed was queried utilize ( antiphonal Oxygen SpeciesMeSH AND Diabetes MellitusMeSH).This query yielded 54 articles as of April 27, 2009. SciMiner, a web-based literature mining tool 14, was used to retrieve and process the abstracts and available beat text documents to identify targets (full text documents were available for approximately 40% of the 1 , 1 54 articles). SciMiner- determine targets, eported in the form of HGNC HUGO (Human Genome Organization) Gene Nomenclature Committee genes, were confirmed by manual(a) polish up of the text. Comparison with human curated data (NCBI Gene2PubMed) The NCBI Gene database provides tie in between Gene and PubMed.The links are the result of (1) manual curation within the NCBI via literature analysis as part of generating a Gene record, (2) integrating of information from other public databases, and (3) GeneRlF (Gene Reference Into Function) in which human experts provide a brief summary of gene functions and make the connections between reference point PubMed) and Gene databases. For the 54 ROS-diabetes articles, gene-paper associations were retrieved from the NCBI Gene database. Non-human genes were mapped to homologous human genes through the NCBI HomoloGene database.The retrieved genes were compared against the SciMiner derived targets. any(prenominal) genes lost by SciMiner were added to the ROS-diabetes target set. Protein-protein fundamental interactions among ROS-diabetes targets To indirectly examine the association of literature derived targets (by SciMiner and NCBI Gene2PubMed) with ROS and diabetes, protein-protein interactions (PPIs) mong the targets were surveyed This was based on an assumption that targets are to a greater extent likely to have PPIs with each other if they are truly associated within the same biological functions/pathways.A PPI net of the ROS-diabetes targets was generated using the sugar Molecular Interactions (MIMI, http//mimi. ncibi. org/ webcite) database 20 and compared against carbon PPI ne cardinalrks of randomly gaunt sets (the same number of the ROS-diabetes target set) from HUGO. A standard Z-test and one type T-test were used to calculate the statistical significance of the ROS- diabetes PPI network with respect to the random PPI networks.Functional enrichment analysis Literature derived ROS-diabetes targets (by SciMiner and NCBI Gene2PubMed) were subject to functional enrichment analyses to identify significantly over-represented biological functions in terms of Gene Ontology 21, pathways (Kyoto Encyclopedia of Genes and Genomes (KEGG, http//www. genome. p/kegg/ webcite) 22 and Reactome http//www. reactome. org/ webcite23). Fishers exact test 24 was used to calculate the statistical significance of these biological functions with BenJamini-Hochberg (BH) adjusted p-value 0. 5 25 as the cut-off. Over-represented ROS-diabetes targets Defining priming corpora To identify a subset of targets that are h ighly over-represented within the ROS- diabetes targets, the frequency of each target (defined as the number of documents in which the target was identified divided by the number of total documents in the query) was compared against the frequencies in randomly selected emphasise corpora.Depending on how the footing set is defined, over-represented targets whitethorn pull up stakes widely therefore, to maintain the background corpora close to the ROS and diabetes context, documents were selected from the same Journal, volume, and issue f the 54 ROS-diabetes documents, but were NOT indexed with responsive Oxygen SpeciesMeSH nor Diabetes MellitusMeSH. For example, one of the ROS-diabetes articles (PMID 18227068), was promulgated in the Journal of biological Chemistry, Volume 283, Issue 16. This issue contained 85 papers, 78 of which were not indexed with either Reactive Oxygen SpeciesMeSH or Diabetes MellitusMeSH indexed.One of these 78 papers was randomly selected as a background d ocument. Three sets of 54 documents were selected using this set about and processed using SciMiner. Identified targets were confirmed by manual review for trueness. Identifying significantly over-represented targets ROS-diabetes targets were tested for over-representation against targets identified from the cardinal background sets. Fishers exact test was used to determine if the frequency of each target in the ROS-diabetes target set was significantly different from that of the background sets. both targets with a BH adjusted p-value 0. 5 in at least two of the three comparisons were deemed to be an over-represented ROS- diabetes target. Functional enrichment analyses were performed on these over- represented ROS-diabetes targets as depict above. Selecting targets tor real time R A subset of targets were selected for RT-PCR from the top 10 over-represented ROS- diabetes targets excluding insulin and NADPH oxidase 5 (NOX5), which does not have a mouse ortholog. Nitric oxide sy nthase 1 (NOSI), the main rootage of nitric oxide, ranked at the 1 5th position and was additionally selected for inclusion in the test set.Differential gene side by real-time RT-PCR Mice DBA/2J mice were purchased from the Jackson Laboratory (Bar Harbor, ME). Mice were housed in a pathogen-free environment and cared for following the University of Michigan Committee on the Care and Use of Animals guidelines. Mice were fed AIN76A chow (Research Diets, unsanded Brunswick, NJ). Male mice were used for this study. Induction of diabetes Two treatment groups were defined reassure (n = 4) and diabetic (n = 4). Diabetes was induced at 13 weeks of age by low-dose streptozotocin (STZ) injections, 50 mg/kg/day for five consecutive days.All diabetic mice genuine LinBit sustained release insulin implants (LinShin, Toronto, Canada) at 8 weeks post-STZ treatment. Insulin implants were replaced every 4 weeks, at 12 and 16 weeks post-STZ treatment. At 20 weeks post-STZ treatment, mice were eu thanized by sodium yellow hornet overdose and DRG were harvested as previously described 26. Real-time RT-PCR The gene expression of the selected nine literature-derived ROS-diabetes targets in DRG was measured using real-time RT-PCR in duplicate.The substance of mRNA isolated from each DRG was normalized to an endogenous reference Tbp TATA box spine protein A cycle threshold (CT). Identification of ROS-diabetes targets A total of 1,021 unmatched targets were identified by SciMiner from the 1,154 ROS- diabetes papers defined by the query of (Reactive Oxygen SpeciesMeSH AND Diabetes MellitusMeSH) and confirmed by manual review. gameboard 1 contains the op 10 most frequently mentioned targets in the ROS-diabetes papers. Insulin was the most frequently mentioned target, followed by superoxide dismutase 1 and catalase. add-in 1 .Top 10 most frequent ROS-diabetes targets The NCBI Gene2PubMed database, containing expert-curated associations between the NCBI Gene and PubMed databases , revealed 90 unique genes associated with the 54 ROS-diabetes papers ( special File 1). SciMiner identified 85 out of these 90 targets, indicating a 94% recall rate. five dollar bill targets missed by SciMiner were added to the initial ROS-diabetes target set to result in 1,026 unique targets (excess File 2). Additional tile 1. The list ot 90 genes trom the NCBI Gene2PubMed database tor the ROS-Diabetes literature (1 , 1 54 papers). arrange XLS surface 35KB transfer consign This load can be viewed with Microsoft outmatch Vieweropen info Additional file 2. The list of 1,026 ROS-Diabetes targets. coif XLS sizing 229KB Download file This file can be viewed with Microsoft outstrip Vieweropen information PPI network of the ROS-diabetes targets The PPI network among the ROS-diabetes targets was evaluated using MIMI interaction data. This was based on the assumption that targets commonly related to certain topic are more likely to have frequent interactions with each other.One h undred PPI networks were generated for comparison using the same number of genes (1,026) randomly selected from the complete HUGO gene set (25,254). The PPI network of the ROS-diabetes targets was significantly different from the randomly generated networks indicating their strong association with the topic ROS and Diabetes. Table 2 demonstrates that the mean number of targets with any PPI interaction in the randomly generated target sets was 528. 9 (approximately 52% of 1,026 targets), piece the number of targets with any PPI interaction in the ROS- iabetes target was 983 (96%).The number of targets interacting with each other was also significantly different between the random networks (mean = 155. 4) and the ROS-diabetes network (mean = 879). Figure 1 illustrates the distributions of these measurements from the 100 random networks with the ROS-diabetes set depicted as a red vertical line. It is obvious that the PPI network of the ROS-diabetes targets is significantly different from the random networks. Table 2. drumhead of 100 randomly generated PPI networks thumbnailFigure 1 . Histograms of randomly generated PPI networks.The histograms llustrate the distributions of 100 randomly generated networks, while the red line indicates the ROS-diabetes targets. The network of the ROS-diabetes targets is significantly different from the 100 randomly generated networks, indicating the converging of ROS-diabetes targets with respect to the topic Reactive Oxygen Species and Diabetes. Functional enrichment analyses of the ROS-diabetes targets Functional enrichment analyses of the 1,026 ROS-diabetes targets were performed to identify over-represented biological functions of the ROS-diabetes targets.After BenJamini-Hochberg correction, a total of 189 molecular functions, 450 biological rocesses, 73 cellular components and 341 pathways were significantly enriched in the ROS-diabetes targets when compared against all the HUGO genes (see Additional Files 3, 4, 5 and 6 f or the full lists). Table 3 lists the top 3 most over-represented GO terms and pathways ranked by p-values of Fishers exact test e. g. , apoptosis, oxidoreductase activity and insulin signaling pathway. Additional file 3. The enriched Molecular Functions Gene Ontology equipment casualty in the 1,026 ROS-Diabetes targets. initialise XLS Size 91 KB Download file This file can be viewed with Microsoft leap out Vieweropen Data Additional file 4. The nriched Biological Processes Gene Ontology Terms in the 1,026 ROS-Diabetes targets. put XLS Size 95KB Download file This tile can be viewed wit Microsott outgo Vieweropen Data Additional tile enriched cellular Components Gene Ontology Terms in the 1,026 ROS-Diabetes targets. Format XLS Size 61 KB Download file This file can be viewed with Microsoft Excel Vieweropen Data Additional file 6. The enriched pathways in the 1,026 ROS-Diabetes targets.Format XLS Size 104KB Download file This file can be viewed with Microsoft Excel Vieweropen Dat a Table 3. Enriched functions of 1,026 ROS-diabetes targets Identification of over-represented ROS-diabetes targets To identify the ROS-diabetes targets highly over-represented in ROS-diabetes literature, three sets of background corpora of the same size (n = 1 , 1 54 documents) were generated using the same Journal, volume and issue approach. The overlap among the three background sets in terms of documents and identified targets are illustrated in Figure 2.Approximately 90% of the selected background documents were unique to the individual set, while 50% of the identified targets were identified in at least one of the three background document sets. The frequencies of the identified targets were compared among the background sets for significant differences. None of the targets had a BH adjusted p-value 0. 05, indicating no significant difference among the targets from the three different background sets (See Additional File 7). thumbnailFigure 2. Venn diagrams of document compos itions and identified targets of the randomly generated background sets.Approximately 90% of the selected background documents were unique to individual set (A), while 50% of the identified targets were identified in at least one of the three background document sets (B). Additional file 7. Comparisons of target frequencies among three background sets. Format XLS Size 22KB Download file This file can be viewed with Microsoft Excel Vieweropen Data Comparisons of the ROS-diabetes targets against these background sets revealed 53 highly over- represented ROS-diabetes targets as listed in Table 4.These 53 targets were significant (p-value 0. 05) against all three background sets and significant following BenJamini-Hochberg multiple testing correction (BH adjusted p-value 0. 05) against at least two of the three background sets. SODI was the most over-represented in he ROS-diabetes targets. Table 4. 53 targets over-represented in ROS-diabetes literature Functional enrichment analyses o f the over-represented ROS-diabetes targets Functional enrichment analyses of the 53 ROS-diabetes targets were performed to identify over- represented biological functions.Following BenJamini-Hochberg correction, a total of 65 molecular functions, 209 biological processes, 26 cellular components and 108 pathways were significantly over-represented when compared against all the HUGO genes (see Additional Files 8, 9, 10 and 11 for the full lists). Table 5 shows the top 3 ost significantly over-represented GO terms and pathways ranked by p-values of Fishers exact test. GO terms related to oxidative stress such as superoxide metabolic process, superoxide release, electron carrier activity and mitochondrion were highly over-represented 53 ROS-diabetes targets Additional file 8.The enriched Molecular Functions Gene Ontology Terms in the Over- represented 53 ROS-Diabetes targets. Format XLS Size 46KB Download file This file can be viewed with Microsoft Excel Vieweropen Data Additional file 9. The enriched Biological Processes Gene Ontology Terms in the Over-represented 53 ROS- Diabetes targets. Format XLS Size 95KB Download file This file can be viewed with Microsoft Excel Vieweropen Data Additional file 10. The enriched Cellular Components Gene Ontology Terms in the Over-represented 53 ROS-Diabetes targets.Format XLS Size 66KB Download file This file can be viewed with Microsoft Excel Vieweropen Data Additional file 1 1 . The enriched pathways in the Over-represented 53 ROS-Diabetes targets. Format XLS Size 75KB Download file This file can be viewed with Microsoft Excel Vieweropen Data Table 5. Enriched functions of the 53 over-represented targets in diabetes Gene expression change in iabetes Two groups of DBA/2J mice exhibited significantly different levels of glycosylated hemoglobin (%GHb). The mean ? SEM were 6. 2 ? 0. for the non-diabetic control group and for 14. 0 ? 0. 8 for the diabetic group (p-value 0. 001), declarative of prolonged hyperglycemia in the d iabetic group 26. DRG were harvested from these animals for gene expression assays. Nine genes were selected from the top ranked ROS-diabetes targets superoxide dismutase 1 (Sodl), catalase (Cat), xanthine dehydrogenase (Xdh), protein kinase C important (Prkca), neutrophil cytosolic factor 1 Ncfl), nitric oxide synthase 3 (Nos3), superoxide dismutase 2 (Sod2), cytochrome b-245 alpha (Cyba), and nitric oxide synthase 1 (Nosl).Eight genes exhibited differential expression between diabetic and non-diabetic mice (p-value 0. 05) as shown in Figure 3. Cat, Sodl, Sod2, Prkca, and NOSI expression levels were diminish, while Ncfl , Xdh, and Cyba expression levels were increased in diabetes. thumbnailFigure 3. Gene expression levels of selected ROS-diabetes targets in DRG examined by real-time RT-PCR. expression levels are relative to Tbp, an internal control (error bar = SEM) (*, p 0. 05 **, p 0. 01 ***, p 0. 01). Eight (Cat, Sodl, Ncfl , Xdh, Sod2, Cyba, Prkca, and Nosl) out of the n ine selected ROS-diabetes genes were significantly regulated by diabetes. Discussion Reactive oxygen species (ROS) are products of normal energy metabolism and play important roles in many other biological processes such as the immune response and signaling cascades 4-6. As mediators of cellular damage, ROS are implicated in pathogenesis of multiple diseases including diabetic complications 27-30.With the aid of literature mining technology, we collected 1 ,026 manageable ROS-related targets from a set of biomedical literature indexed with both ROS and diabetes. Fifty-three targets were significantly over-represented in the ROS-diabetes papers when compared against three background sets. Depending on how the background set is defined, the over-represented targets may vary widely. An high-flown background set would be the entire PubMed set however, this is not possible due to limited access to tull texts and intense data processing.An alternative order wou d be to use only abstrac ts in PubMed, but this may not fully represent the literature. Using only the abstracts, our target identification method resulted in 21 (39%) of the 53 key ROS- iabetes targets (Additional File 12), suggesting the eudaimonia of rich information in full text documents. In the present study, background documents were randomly selected from the same Journal, volume, and issue of the 54 ROS-diabetes documents, which were not indexed with Reactive Oxygen SpeciesMeSH nor Diabetes MellitusMeSH.This approach maintained the background corpora not far from the ROS and diabetes context. Additional file 12. The Key 53 ROS-Diabetes Targets Identifiable Using Only the Abstracts. Format XLS Size 23KB Download file This file can be viewed with Microsoft Excel Vieweropen Data The gene expression evels of nine targets selected from the 53 over-represented ROS-diabetes targets were measured in diabetic and non-diabetic DRG. Our laboratory is particularly interested in deciphering the underlying mech anisms of diabetic neuropathy, a major complication of diabetes.Data print by our laboratory both in vitro and in vivo confirm the negative impact of oxidative stress in complication-prone neuron tissues like DRG In an effort to obtain diabetic neuropathy specific targets, SciMiner was employed to further analyze a subset of the ROS-diabetes papers (data not shown). Nerve growth factor (NGF) was identified as the most over- epresented target in this subset when compared to the full ROS-diabetes set however, NGF did not have statistical significance (BH adjusted p-value = 0. 06). The relatively small numbers of papers and associated targets may have contributed to this non-significance.Therefore, the candidate targets for gene expression validation were selected from among the 53 over-represented ROS-diabetes targets derived from the full ROS-diabetes corpus. Among the tested genes, the expression levels of Cat, Sodl , Sod2, Prkca, and NOSI were decreased, while the expression level s of Ncfl , Xdh, and Cyba were increased nder diabetic conditions. Cat, Sodl , and Sod2 are responsible for protecting cells from oxidative stress by destroying superoxides and hydrogen peroxides 8-11. lessen expression of these genes may result in oxidative stress 32.Increased expression of Cyba and Ncfl , subunits of superoxide-generating nicotinamide adenine dinucleotide phosphate (NADPH) oxidase complex 30, also supports enhanced oxidative stress. Xdh and its inter-convertible form, Xanthine oxidase (Xod), showed increased activity in various rat tissues under oxidative stress conditions ith diabetes 33, and also showed increased expression in diabetic DRG in the current study. Unlike the above concordant genes, protein kinase C and nitric oxide synthases did not exhibit predicted expression changes in diabetes.Protein kinase C activates NADPH oxidase, further promoting oxidative stress in the cell 34,35. Decreased expression of Prkca in our diabetic DRG is not parallel with ex pression levels of other enzymes judge to increase oxidative stress. Between the two nitric oxide synthases tested in the present study, NOSI (neuronal) expression was significantly decreased (p-value 0. 01) in diabetes, while Nos3 (endothelial) expression was not significant (p-value = 0. 06). The neuronal NOSI is expected to play a major role in producing nitric oxide, other type of highly reactive free radical.Thus, with some exceptions, the majority of the differentially expressed genes in DRG show parallel results to the known activities of these targets in diabetes, suggesting enhanced oxidative stress in the diabetic DRG. Assessment of antioxidant enzyme expression in diabetes has yielded a variety of results 36-40 depending upon the duration of diabetes, the tissue studied and other factors. In diabetic mice and rats, it is commonly reported that superoxide dismutases are down-regulated 37-40, where data regarding catalase are variable 36,40.PKC is activated in diabetes, but most papers that examined mRNA demonstrated that its expression is largely unchanged 41. Among the 53 over-represented ROS-diabetes targets, SODI was the most over- represented and was differentially expressed under diabetic and non-diabetic conditions. To the best of our knowledge, no published study has investigated the role of SODI in the onset and/or progression of diabetic neuropathy. Mutations of SODI have long been associated with the inherited form of amyotrophic lateral sclerosis (ALS) 42 and the possibleness of oxidative stress-based aging 43.Early reports indicate that knockout of the SODI gene does not print nervous system development 44, although recovery following injury is easily and incomplete 45,46. With respect to diabetes, SODI KO accelerates the development of diabetic nephropathy 47 and cataract formation 48. Thus, examining the SODI KO mouse as a model of diabetic neuropathy would be a reasonable follow-up study. One limitation of the current approach us ing literature mining technology is incorrect r missed identification of the mentioned targets within the literature.Based on a performance evaluation using a standard text set BioCreAtlvE (Critical Assessment of Information origin systems in Biology) version 2 49, SciMiner achieved 87. 1% recall (percentage identification of targets in the given text), 71. 3% precision (percentage accuracy of identified target) and 75. 8% F-measure (harmonious add up of recall and precision = (2 x recall x precision)/(recall + precision)) before manual revision 14. In order to improve the accuracy of SciMiners results, each target was anually reviewed and corrected by checking the sentences in which each target was identified.Approximately, 120 targets (10% of the initially identified targets from the ROS-diabetes papers) were removed during the manual review process. The overall accuracy is expected to improve through the review process however, the review process did not address targets missed b y SciMiner, since we did not thoroughly review individual papers. Instead, 5 missed targets, whose associations with ROS-diabetes literature were available in the NCBI Gene2PubMed database, were added to the closing ROS-diabetes target list (Additional File 2).