Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API.
<h4>Background</h4>Biochemical pathways provide an essential context for understanding comprehensive experimental data and the systematic workings of a cell. Therefore, the availability of online pathway browsers will facilitate post-genomic research, just as genome browsers have contrib...
Guardado en:
| Autores principales: | , , , , , , , |
|---|---|
| Formato: | article |
| Lenguaje: | EN |
| Publicado: |
Public Library of Science (PLoS)
2009
|
| Materias: | |
| Acceso en línea: | https://doaj.org/article/b50bbdc7ab78458db911bb1a8e4d9285 |
| Etiquetas: |
Agregar Etiqueta
Sin Etiquetas, Sea el primero en etiquetar este registro!
|
| id |
oai:doaj.org-article:b50bbdc7ab78458db911bb1a8e4d9285 |
|---|---|
| record_format |
dspace |
| spelling |
oai:doaj.org-article:b50bbdc7ab78458db911bb1a8e4d92852021-11-25T06:28:12ZPathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API.1932-620310.1371/journal.pone.0007710https://doaj.org/article/b50bbdc7ab78458db911bb1a8e4d92852009-11-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19907644/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Biochemical pathways provide an essential context for understanding comprehensive experimental data and the systematic workings of a cell. Therefore, the availability of online pathway browsers will facilitate post-genomic research, just as genome browsers have contributed to genomics. Many pathway maps have been provided online as part of public pathway databases. Most of these maps, however, function as the gateway interface to a specific database, and the comprehensiveness of their represented entities, data mapping capabilities, and user interfaces are not always sufficient for generic usage.<h4>Methodology/principal findings</h4>We have identified five central requirements for a pathway browser: (1) availability of large integrated maps showing genes, enzymes, and metabolites; (2) comprehensive search features and data access; (3) data mapping for transcriptomic, proteomic, and metabolomic experiments, as well as the ability to edit and annotate pathway maps; (4) easy exchange of pathway data; and (5) intuitive user experience without the requirement for installation and regular maintenance. According to these requirements, we have evaluated existing pathway databases and tools and implemented a web-based pathway browser named Pathway Projector as a solution.<h4>Conclusions/significance</h4>Pathway Projector provides integrated pathway maps that are based upon the KEGG Atlas, with the addition of nodes for genes and enzymes, and is implemented as a scalable, zoomable map utilizing the Google Maps API. Users can search pathway-related data using keywords, molecular weights, nucleotide sequences, and amino acid sequences, or as possible routes between compounds. In addition, experimental data from transcriptomic, proteomic, and metabolomic analyses can be readily mapped. Pathway Projector is freely available for academic users at (http://www.g-language.org/PathwayProjector/).Nobuaki KonoKazuharu ArakawaRyu OgawaNobuhiro KidoKazuki OshitaKeita IkegamiSatoshi TamakiMasaru TomitaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 4, Iss 11, p e7710 (2009) |
| institution |
DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
Medicine R Science Q |
| spellingShingle |
Medicine R Science Q Nobuaki Kono Kazuharu Arakawa Ryu Ogawa Nobuhiro Kido Kazuki Oshita Keita Ikegami Satoshi Tamaki Masaru Tomita Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API. |
| description |
<h4>Background</h4>Biochemical pathways provide an essential context for understanding comprehensive experimental data and the systematic workings of a cell. Therefore, the availability of online pathway browsers will facilitate post-genomic research, just as genome browsers have contributed to genomics. Many pathway maps have been provided online as part of public pathway databases. Most of these maps, however, function as the gateway interface to a specific database, and the comprehensiveness of their represented entities, data mapping capabilities, and user interfaces are not always sufficient for generic usage.<h4>Methodology/principal findings</h4>We have identified five central requirements for a pathway browser: (1) availability of large integrated maps showing genes, enzymes, and metabolites; (2) comprehensive search features and data access; (3) data mapping for transcriptomic, proteomic, and metabolomic experiments, as well as the ability to edit and annotate pathway maps; (4) easy exchange of pathway data; and (5) intuitive user experience without the requirement for installation and regular maintenance. According to these requirements, we have evaluated existing pathway databases and tools and implemented a web-based pathway browser named Pathway Projector as a solution.<h4>Conclusions/significance</h4>Pathway Projector provides integrated pathway maps that are based upon the KEGG Atlas, with the addition of nodes for genes and enzymes, and is implemented as a scalable, zoomable map utilizing the Google Maps API. Users can search pathway-related data using keywords, molecular weights, nucleotide sequences, and amino acid sequences, or as possible routes between compounds. In addition, experimental data from transcriptomic, proteomic, and metabolomic analyses can be readily mapped. Pathway Projector is freely available for academic users at (http://www.g-language.org/PathwayProjector/). |
| format |
article |
| author |
Nobuaki Kono Kazuharu Arakawa Ryu Ogawa Nobuhiro Kido Kazuki Oshita Keita Ikegami Satoshi Tamaki Masaru Tomita |
| author_facet |
Nobuaki Kono Kazuharu Arakawa Ryu Ogawa Nobuhiro Kido Kazuki Oshita Keita Ikegami Satoshi Tamaki Masaru Tomita |
| author_sort |
Nobuaki Kono |
| title |
Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API. |
| title_short |
Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API. |
| title_full |
Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API. |
| title_fullStr |
Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API. |
| title_full_unstemmed |
Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API. |
| title_sort |
pathway projector: web-based zoomable pathway browser using kegg atlas and google maps api. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2009 |
| url |
https://doaj.org/article/b50bbdc7ab78458db911bb1a8e4d9285 |
| work_keys_str_mv |
AT nobuakikono pathwayprojectorwebbasedzoomablepathwaybrowserusingkeggatlasandgooglemapsapi AT kazuharuarakawa pathwayprojectorwebbasedzoomablepathwaybrowserusingkeggatlasandgooglemapsapi AT ryuogawa pathwayprojectorwebbasedzoomablepathwaybrowserusingkeggatlasandgooglemapsapi AT nobuhirokido pathwayprojectorwebbasedzoomablepathwaybrowserusingkeggatlasandgooglemapsapi AT kazukioshita pathwayprojectorwebbasedzoomablepathwaybrowserusingkeggatlasandgooglemapsapi AT keitaikegami pathwayprojectorwebbasedzoomablepathwaybrowserusingkeggatlasandgooglemapsapi AT satoshitamaki pathwayprojectorwebbasedzoomablepathwaybrowserusingkeggatlasandgooglemapsapi AT masarutomita pathwayprojectorwebbasedzoomablepathwaybrowserusingkeggatlasandgooglemapsapi |
| _version_ |
1718413705160425472 |