Automated genomic variant literature search engines and a comparison of the results with PubMed and PMC
| Search Engine . | Variant normalization . | QE (normalizes the query) . | Content scope . | Evaluation . | URL . | Publicly available? . | Last updatea . | |||
|---|---|---|---|---|---|---|---|---|---|---|
| ‘BRAF p.V600E’ resultsa . | ‘KRAS p.G12D’ resultsa . | ‘XRCC2 p.R188H’ resultsa . | ‘KCNH2 p.L552S’ resultsa . | |||||||
| LitVar [50] | tmVar, GNormPlus | Yes | Title, abstract, full text (PubMed and PMC Open Access Subset) | 13 987 | 4940 | 110 | 12 | https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/LitVar | Yes | May 2020 |
| Variant2Literature [73] | tmVar, GNormPlus | Yes | Title, abstract, full text, supplementary (PubMed and PMC Open Access Subset) | 8473 | 3318 | 108 | 9 | https://variant2literature.taigenomics.com | Yes | February 2020 |
| VIST [52] | tmVar, GNormPlus (Through PubTator) | No | Title, abstract (PubMed) | 111 (BRAF p.V600E) 2898 (BRAF V600E) | 33 (KRAS p.G12D) 519 (KRAS G12D) | 0 (XRCC2 p.R188H) 21 (XRCC2 R188H) | 0 (KCNH2 p.L552S) 5 (KCNH2 L552S) | https://vist.informatik.hu-berlin.de | Yes | 2018 |
| BEST [55] | tmVar | No | Title, abstract (PubMed) | 133 (BRAF p.V600E) 3224 (BRAF V600E) | 35 (KRAS p.G12D) 556 (KRAS G12D) | 0 (XRCC2 p.R188H) 21 (XRCC2 R188H) | 0 (KCNH2 p.L552S) 3 (KCNH2 L552S) | http://best.korea.ac.kr | Yes | May 2020 |
| GeneView [56] | SETH and GNAT | No | Title, abstract, full-text (PubMed and PMC Open Access Subset) | 45 (MUTATION:p.V600E AND ENTREZ:673) 1010 (MUTATION:V600E AND ENTREZ:673) | 4 (MUTATION: p.G12D AND ENTREZ: 3845) 40 (MUTATION: G12D AND ENTREZ: 3845) | 1 (MUTATION:p.R188H AND ENTREZ:7516) 51 (MUTATION:R188H AND ENTREZ:7516) | 2 (MUTATION:p.L552S AND ENTREZ:3757) 5 (MUTATION:L552S AND ENTREZ:3757) | http://bc3.informatik.hu-berlin.de/ | Yes | 2017 |
| Mastermind [57] | Unknown | Yes | Title, abstract, full text (Unknown) | 20 047 | 5568 | 229 | 47 | https://mastermind.genomenon.com/ | Limited | May 2020 |
| PubMed | N/A | No | Title, abstract | 146 (BRAF p.V600E) 4402 (BRAF V600E) | 49 (KRAS p.G12D) 1004 (KRAS G12D) | 0 (XRCC2 p.R188H) 21 (XRCC2 R188H) | 0 (KCNH2 p.L552S) 5 (KCNH2 L552S) | https://www.ncbi.nlm.nih.gov/pubmed | Yes | Updated daily |
| PMC | N/A | No | Title, abstract, full text | 446 (BRAF p.V600E) 11918 (BRAF V600E) | 323 (KRAS p.G12D) 4603 (KRAS G12D) | 1 (XRCC2 p.R188H) 54 (XRCC2 R188H) | 2 (KCNH2 p.L552S) 6 (KCNH2 L552S) | https://www.ncbi.nlm.nih.gov/pmc | Yes | Updated daily |
| Search Engine . | Variant normalization . | QE (normalizes the query) . | Content scope . | Evaluation . | URL . | Publicly available? . | Last updatea . | |||
|---|---|---|---|---|---|---|---|---|---|---|
| ‘BRAF p.V600E’ resultsa . | ‘KRAS p.G12D’ resultsa . | ‘XRCC2 p.R188H’ resultsa . | ‘KCNH2 p.L552S’ resultsa . | |||||||
| LitVar [50] | tmVar, GNormPlus | Yes | Title, abstract, full text (PubMed and PMC Open Access Subset) | 13 987 | 4940 | 110 | 12 | https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/LitVar | Yes | May 2020 |
| Variant2Literature [73] | tmVar, GNormPlus | Yes | Title, abstract, full text, supplementary (PubMed and PMC Open Access Subset) | 8473 | 3318 | 108 | 9 | https://variant2literature.taigenomics.com | Yes | February 2020 |
| VIST [52] | tmVar, GNormPlus (Through PubTator) | No | Title, abstract (PubMed) | 111 (BRAF p.V600E) 2898 (BRAF V600E) | 33 (KRAS p.G12D) 519 (KRAS G12D) | 0 (XRCC2 p.R188H) 21 (XRCC2 R188H) | 0 (KCNH2 p.L552S) 5 (KCNH2 L552S) | https://vist.informatik.hu-berlin.de | Yes | 2018 |
| BEST [55] | tmVar | No | Title, abstract (PubMed) | 133 (BRAF p.V600E) 3224 (BRAF V600E) | 35 (KRAS p.G12D) 556 (KRAS G12D) | 0 (XRCC2 p.R188H) 21 (XRCC2 R188H) | 0 (KCNH2 p.L552S) 3 (KCNH2 L552S) | http://best.korea.ac.kr | Yes | May 2020 |
| GeneView [56] | SETH and GNAT | No | Title, abstract, full-text (PubMed and PMC Open Access Subset) | 45 (MUTATION:p.V600E AND ENTREZ:673) 1010 (MUTATION:V600E AND ENTREZ:673) | 4 (MUTATION: p.G12D AND ENTREZ: 3845) 40 (MUTATION: G12D AND ENTREZ: 3845) | 1 (MUTATION:p.R188H AND ENTREZ:7516) 51 (MUTATION:R188H AND ENTREZ:7516) | 2 (MUTATION:p.L552S AND ENTREZ:3757) 5 (MUTATION:L552S AND ENTREZ:3757) | http://bc3.informatik.hu-berlin.de/ | Yes | 2017 |
| Mastermind [57] | Unknown | Yes | Title, abstract, full text (Unknown) | 20 047 | 5568 | 229 | 47 | https://mastermind.genomenon.com/ | Limited | May 2020 |
| PubMed | N/A | No | Title, abstract | 146 (BRAF p.V600E) 4402 (BRAF V600E) | 49 (KRAS p.G12D) 1004 (KRAS G12D) | 0 (XRCC2 p.R188H) 21 (XRCC2 R188H) | 0 (KCNH2 p.L552S) 5 (KCNH2 L552S) | https://www.ncbi.nlm.nih.gov/pubmed | Yes | Updated daily |
| PMC | N/A | No | Title, abstract, full text | 446 (BRAF p.V600E) 11918 (BRAF V600E) | 323 (KRAS p.G12D) 4603 (KRAS G12D) | 1 (XRCC2 p.R188H) 54 (XRCC2 R188H) | 2 (KCNH2 p.L552S) 6 (KCNH2 L552S) | https://www.ncbi.nlm.nih.gov/pmc | Yes | Updated daily |
aEvaluated in May 2020.
Automated genomic variant literature search engines and a comparison of the results with PubMed and PMC
| Search Engine . | Variant normalization . | QE (normalizes the query) . | Content scope . | Evaluation . | URL . | Publicly available? . | Last updatea . | |||
|---|---|---|---|---|---|---|---|---|---|---|
| ‘BRAF p.V600E’ resultsa . | ‘KRAS p.G12D’ resultsa . | ‘XRCC2 p.R188H’ resultsa . | ‘KCNH2 p.L552S’ resultsa . | |||||||
| LitVar [50] | tmVar, GNormPlus | Yes | Title, abstract, full text (PubMed and PMC Open Access Subset) | 13 987 | 4940 | 110 | 12 | https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/LitVar | Yes | May 2020 |
| Variant2Literature [73] | tmVar, GNormPlus | Yes | Title, abstract, full text, supplementary (PubMed and PMC Open Access Subset) | 8473 | 3318 | 108 | 9 | https://variant2literature.taigenomics.com | Yes | February 2020 |
| VIST [52] | tmVar, GNormPlus (Through PubTator) | No | Title, abstract (PubMed) | 111 (BRAF p.V600E) 2898 (BRAF V600E) | 33 (KRAS p.G12D) 519 (KRAS G12D) | 0 (XRCC2 p.R188H) 21 (XRCC2 R188H) | 0 (KCNH2 p.L552S) 5 (KCNH2 L552S) | https://vist.informatik.hu-berlin.de | Yes | 2018 |
| BEST [55] | tmVar | No | Title, abstract (PubMed) | 133 (BRAF p.V600E) 3224 (BRAF V600E) | 35 (KRAS p.G12D) 556 (KRAS G12D) | 0 (XRCC2 p.R188H) 21 (XRCC2 R188H) | 0 (KCNH2 p.L552S) 3 (KCNH2 L552S) | http://best.korea.ac.kr | Yes | May 2020 |
| GeneView [56] | SETH and GNAT | No | Title, abstract, full-text (PubMed and PMC Open Access Subset) | 45 (MUTATION:p.V600E AND ENTREZ:673) 1010 (MUTATION:V600E AND ENTREZ:673) | 4 (MUTATION: p.G12D AND ENTREZ: 3845) 40 (MUTATION: G12D AND ENTREZ: 3845) | 1 (MUTATION:p.R188H AND ENTREZ:7516) 51 (MUTATION:R188H AND ENTREZ:7516) | 2 (MUTATION:p.L552S AND ENTREZ:3757) 5 (MUTATION:L552S AND ENTREZ:3757) | http://bc3.informatik.hu-berlin.de/ | Yes | 2017 |
| Mastermind [57] | Unknown | Yes | Title, abstract, full text (Unknown) | 20 047 | 5568 | 229 | 47 | https://mastermind.genomenon.com/ | Limited | May 2020 |
| PubMed | N/A | No | Title, abstract | 146 (BRAF p.V600E) 4402 (BRAF V600E) | 49 (KRAS p.G12D) 1004 (KRAS G12D) | 0 (XRCC2 p.R188H) 21 (XRCC2 R188H) | 0 (KCNH2 p.L552S) 5 (KCNH2 L552S) | https://www.ncbi.nlm.nih.gov/pubmed | Yes | Updated daily |
| PMC | N/A | No | Title, abstract, full text | 446 (BRAF p.V600E) 11918 (BRAF V600E) | 323 (KRAS p.G12D) 4603 (KRAS G12D) | 1 (XRCC2 p.R188H) 54 (XRCC2 R188H) | 2 (KCNH2 p.L552S) 6 (KCNH2 L552S) | https://www.ncbi.nlm.nih.gov/pmc | Yes | Updated daily |
| Search Engine . | Variant normalization . | QE (normalizes the query) . | Content scope . | Evaluation . | URL . | Publicly available? . | Last updatea . | |||
|---|---|---|---|---|---|---|---|---|---|---|
| ‘BRAF p.V600E’ resultsa . | ‘KRAS p.G12D’ resultsa . | ‘XRCC2 p.R188H’ resultsa . | ‘KCNH2 p.L552S’ resultsa . | |||||||
| LitVar [50] | tmVar, GNormPlus | Yes | Title, abstract, full text (PubMed and PMC Open Access Subset) | 13 987 | 4940 | 110 | 12 | https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/LitVar | Yes | May 2020 |
| Variant2Literature [73] | tmVar, GNormPlus | Yes | Title, abstract, full text, supplementary (PubMed and PMC Open Access Subset) | 8473 | 3318 | 108 | 9 | https://variant2literature.taigenomics.com | Yes | February 2020 |
| VIST [52] | tmVar, GNormPlus (Through PubTator) | No | Title, abstract (PubMed) | 111 (BRAF p.V600E) 2898 (BRAF V600E) | 33 (KRAS p.G12D) 519 (KRAS G12D) | 0 (XRCC2 p.R188H) 21 (XRCC2 R188H) | 0 (KCNH2 p.L552S) 5 (KCNH2 L552S) | https://vist.informatik.hu-berlin.de | Yes | 2018 |
| BEST [55] | tmVar | No | Title, abstract (PubMed) | 133 (BRAF p.V600E) 3224 (BRAF V600E) | 35 (KRAS p.G12D) 556 (KRAS G12D) | 0 (XRCC2 p.R188H) 21 (XRCC2 R188H) | 0 (KCNH2 p.L552S) 3 (KCNH2 L552S) | http://best.korea.ac.kr | Yes | May 2020 |
| GeneView [56] | SETH and GNAT | No | Title, abstract, full-text (PubMed and PMC Open Access Subset) | 45 (MUTATION:p.V600E AND ENTREZ:673) 1010 (MUTATION:V600E AND ENTREZ:673) | 4 (MUTATION: p.G12D AND ENTREZ: 3845) 40 (MUTATION: G12D AND ENTREZ: 3845) | 1 (MUTATION:p.R188H AND ENTREZ:7516) 51 (MUTATION:R188H AND ENTREZ:7516) | 2 (MUTATION:p.L552S AND ENTREZ:3757) 5 (MUTATION:L552S AND ENTREZ:3757) | http://bc3.informatik.hu-berlin.de/ | Yes | 2017 |
| Mastermind [57] | Unknown | Yes | Title, abstract, full text (Unknown) | 20 047 | 5568 | 229 | 47 | https://mastermind.genomenon.com/ | Limited | May 2020 |
| PubMed | N/A | No | Title, abstract | 146 (BRAF p.V600E) 4402 (BRAF V600E) | 49 (KRAS p.G12D) 1004 (KRAS G12D) | 0 (XRCC2 p.R188H) 21 (XRCC2 R188H) | 0 (KCNH2 p.L552S) 5 (KCNH2 L552S) | https://www.ncbi.nlm.nih.gov/pubmed | Yes | Updated daily |
| PMC | N/A | No | Title, abstract, full text | 446 (BRAF p.V600E) 11918 (BRAF V600E) | 323 (KRAS p.G12D) 4603 (KRAS G12D) | 1 (XRCC2 p.R188H) 54 (XRCC2 R188H) | 2 (KCNH2 p.L552S) 6 (KCNH2 L552S) | https://www.ncbi.nlm.nih.gov/pmc | Yes | Updated daily |
aEvaluated in May 2020.
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