New concepts for building vocabulary for cell image ontologies

BMC Bioinformatics

Volumn 12, Issue 1, 2011, Pages

  Plant, Anne L ^a   Elliott, John T ^a   Bhat, Talapady N ^a  

^a NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL BIOLOGY; CELL IMAGES; CELL IMAGING; DATABASE TECHNOLOGY; EXPERIMENTAL PARAMETERS; QUERY DATUM; SEARCH TERMS; XML SCHEMAS;

CELL CULTURE; CELLS; COMPUTER SOFTWARE REUSABILITY; EXPERIMENTS; FORESTRY; MATERIALS HANDLING; METADATA; QUERY LANGUAGES; QUERY PROCESSING;

TREES (MATHEMATICS);

ANIMAL; ARTICLE; CELL LINE; CELL STRAIN 3T3; CYTOLOGY; FACTUAL DATABASE; FIBROBLAST; INTERNET; LINGUISTICS; MOUSE; RAT; SEMANTICS; SMOOTH MUSCLE FIBER;

ANIMALS; CELL LINE; DATABASES, FACTUAL; FIBROBLASTS; INTERNET; MICE; MYOCYTES, SMOOTH MUSCLE; NIH 3T3 CELLS; RATS; SEMANTICS; VOCABULARY, CONTROLLED;

EID: 83755228921     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-487     Document Type: Article

References (36)

1. Giuliano KA, Haskins JR, Taylor DL. Advances in high content screening for drug discovery. Assay and drug development technologies 2003, 1(4):565-577. 10.1089/154065803322302826, 15090253.
2. Price JH, Goodacre A, Hahn K, Hodgson L, Hunter EA, Krajewski S, Murphy RF, Rabinovich A, Reed JC, Heynen S. Advances in molecular labeling, high throughput imaging and machine intelligence portend powerful functional cellular biochemistry tools. Journal of cellular biochemistry 2002, 39:194-210.
3. Carpenter AE. Extracting rich information from images. Methods in molecular biology Clifton, NJ 2009, 486:193-211.
4. Swedlow JR, Goldberg IG, Eliceiri KW. Bioimage informatics for experimental biology. Annual review of biophysics 2009, 38:327-346. 10.1146/annurev.biophys.050708.133641, 19416072.
5. Goldberg IG, Allan C, Burel JM, Creager D, Falconi A, Hochheiser H, Johnston J, Mellen J, Sorger PK, Swedlow JR. The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging. Genome biology 2005, 6(5):R47. 10.1186/gb-2005-6-5-r47, 1175959, 15892875.
6. Glory E, Murphy RF. Automated subcellular location determination and high-throughput microscopy. Developmental cell 2007, 12(1):7-16. 10.1016/j.devcel.2006.12.007, 17199037.
7. Martone ME, Zhang S, Gupta A, Qian X, He H, Price DL, Wong M, Santini S, Ellisman MH. The cell-centered database: a database for multiscale structural and protein localization data from light and electron microscopy. Neuroinformatics 2003, 1(4):379-395. 10.1385/NI:1:4:379, 15043222.
8. Linkert M, Rueden CT, Allan C, Burel JM, Moore W, Patterson A, Loranger B, Moore J, Neves C, Macdonald D, et al. Metadata matters: access to image data in the real world. The Journal of cell biology 189(5):777-782.
9. Kvilekval K, Fedorov D, Obara B, Singh A, Manjunath BS. Bisque: a platform for bioimage analysis and management. Bioinformatics (Oxford, England) 26(4):544-552.
10. Vannier MW, Summers RM. Sharing images. Radiology 2003, 228(1):23-25. 10.1148/radiol.2281021654, 12832571.
11. Boyle J, Rovira H, Cavnor C, Burdick D, Killcoyne S, Shmulevich I. Adaptable data management for systems biology investigations. BMC bioinformatics 2009, 10:79. 10.1186/1471-2105-10-79, 2670281, 19265554.
12. Ruttenberg A, Clark T, Bug W, Samwald M, Bodenreider O, Chen H, Doherty D, Forsberg K, Gao Y, Kashyap V, et al. Advancing translational research with the Semantic Web. BMC bioinformatics 2007, 8(Suppl 3):S2. 10.1186/1471-2105-8-S3-S2, 2230503, 18269696.
13. Staab E, Clarke LP, Baker H, Sullivan D. NCI image archive management workshop: a preliminary report. Academic radiology 2001, 8(7):690-691. 10.1016/S1076-6332(03)80699-2, 11450970.
14. MIACA - Minimum Information About a Cellular Assay. , http://miaca.sourceforge.net/
15. Lee JA, Spidlen J, Boyce K, Cai J, Crosbie N, Dalphin M, Furlong J, Gasparetto M, Goldberg M, Goralczyk EM, et al. MIFlowCyt: the minimum information about a Flow Cytometry Experiment. Cytometry A 2008, 73(10):926-930. 2773297, 18752282.
16. Minimal Information About T cell Assays ("MIATA"). , http://www.miataproject.org/
17. Janetzki S, Britten CM, Kalos M, Levitsky HI, Maecker HT, Melief CJ, Old LJ, Romero P, Hoos A, Davis MM. "MIATA"-minimal information about T cell assays. Immunity 2009, 31(4):527-528. 10.1016/j.immuni.2009.09.007, 19833080.
18. Bard J, Rhee SY, Ashburner M. An ontology for cell types. Genome biology 2005, 6(2):R21. 10.1186/gb-2005-6-2-r21, 551541, 15693950.
19. Microarray Gene Expression Data. , http://mged.sourceforge.net
20. The Open Microscopy Environment. , http://www.openmicroscopy.org/site
21. Jameson D, Turner DA, Ankers J, Kennedy S, Ryan S, Swainston N, Griffiths T, Spiller DG, Oliver SG, White MR, et al. Information management for high content live cell imaging. BMC bioinformatics 2009, 10:226. 10.1186/1471-2105-10-226, 2723092, 19622144.
22. Splendiani A. RDFScape: Semantic Web meets systems biology. BMC bioinformatics 2008, 9(Suppl 4):S6. 10.1186/1471-2105-9-S4-S6, 2638146, 19091029.
23. Scheuermann R, Kong M, Dahlke C, Cai J, Lee J, Qian Y, Squires Dunn P, Wiser J, Hagler H, Smith B, Karp D. Ontology-based Knowledge Representation of Experiment Metadata in Biological Data Mining. Biological data mining 2009, 529-559. Boca Raton FL: Chapman & Hall/CRC, Chen J, Lonardi S.
24. Ruch P, Gobeill J, Lovis C, Geissbuhler A. Automatic medical encoding with SNOMED categories. BMC medical informatics and decision making 2008, 8(Suppl 1):S6. 10.1186/1472-6947-8-S1-S6, 2582793, 19007443.
25. Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, et al. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature biotechnology 2007, 25(11):1251-1255. 10.1038/nbt1346, 2814061, 17989687.
26. Smedley D, Haider S, Ballester B, Holland R, London D, Thorisson G, Kasprzyk A. BioMart--biological queries made easy. BMC genomics 2009, 10:22. 10.1186/1471-2164-10-22, 2649164, 19144180.
27. The Cell: an Image Library. , http://cellimagelibrary.org/
28. Kvilekval K, Fedorov D, Obara B, Singh A, Manjunath BS. Bisque: a platform for bioimage analysis and management. Bioinformatics (Oxford, England) 2010, 26(4):544-552.
29. Prasanna MD, Vondrasek J, Wlodawer A, Rodriguez H, Bhat TN. Chemical compound navigator: a web-based chem-BLAST, chemical taxonomy-based search engine for browsing compounds. Proteins 2006, 63(4):907-917. 10.1002/prot.20914, 16508960.
30. Degtyarenko K, de Matos P, Ennis M, Hastings J, Zbinden M, McNaught A, Alcantara R, Darsow M, Guedj M, Ashburner M. ChEBI: a database and ontology for chemical entities of biological interest. Nucleic acids research 2008, (36 Database):D344-350.
31. Coles SJ, Day NE, Murray-Rust P, Rzepa HS, Zhang Y. Enhancement of the chemical semantic web through the use of InChI identifiers. Organic & biomolecular chemistry 2005, 3(10):1832-1834. 10.1039/b502828k, 3249303, 22263152.
32. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature genetics 2000, 25(1):25-29. 10.1038/75556, 3037419, 10802651.
33. Sansone SA, Rocca-Serra P, Brandizi M, Brazma A, Field D, Fostel J, Garrow AG, Gilbert J, Goodsaid F, Hardy N, et al. The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?". Omics 2008, 12(2):143-149. 10.1089/omi.2008.0019, 18447634.
34. Bhat TN, Barkley J. Semantic Web for the Life Sciences - Hype, Why, How and Use Case for AIDS Inhibitors. IEEE Congress on Services 2007, 87-91.
35. Bhat TN. Building Chemical Ontology for Semantic Web Using Substructures Created by Chem-BLAST. JSWIS 2010, 6(3):22-37.
36. Dima JAE, Filliben J, Halter M, Peskin A, Bernal J, Kociolek M, Brady M, Tang H, Plant A. Comparison of segmentation algorithms for fluorescence microscopy images of cells (Submitted for Publication). 2010,