Annotating papers in computational pathology

[ArtPoon]

I found an "ontology" (defined set of concepts and categories) for bioinformatics that's being developed here. I'm extracting the highest-level terms for Operation (method) and Data, it would be really useful to note which of these are relevant to each of the papers that you're going to review.

Data

• Alignment
• Codon usage
• Data index (genome index - generating a "look up table" of a reference genome to apply to sequence data from a similar genome)
• Data reference (mapping data to another database)
• Database search results
• Ecological data
• Evidence
• Experimental measurements
• Gene expression data
• Hierarchy (data describing a biological hierarchy)
• Identifier (labels for data)
• Image
• Keyword (e.g., text searching publication databases)
• Map data (genetic, physical) - where things are located
• Mathematical model
• Matrix (such as a distance matrix)
• Molecular property (such as amino acid charge or protein stability)
• Ontology data (a system like this one)
• Pathway or network
• Phylogeny
• Plots
• Query script (a method for searching a database)
• Reaction data (enzyme kinetics)
• Report (the content of some document generated by a program or person)
• Score (a measure of similarity in comparing data, or a statistical test)
• Sequence (nucleotide, protein; attributes, features, variations)
• Spectrum (NMR)
• Structure (molecular; profile)
• Taxonomy (hierarchical classification of organisms/species)
• Text data (article, abstract, bibliography)
• Training material

Operation (methods)

• Alignment
• Analysis
• Annotation
• Anonymization
• Assembly
• Calculation
• Classification
• Clustering
• Comparison
• Conversion
• Correlation
• Data handling
• Deposition
• Design (e.g., design a custom protein with desired properties)
• Generation (construct data)
• Indexing (generate an index of a database)
• Mapping (locate something to a genome or structure)
• Modelling and simulation
• Optimisation and refinement
• Plotting
• Prediction and recognition
• Query and retrival
• Service management (concerning the handling and use of other tools)
• Validation (quality control)
• Visualization

Let me know if you need any help interpreting these terms!

[ArtPoon]

Searching PubMed for the phrase "computational pathology" only returns 25 articles:

1. Kumar N, Verma R, Sharma S, Bhargava S, Vahadane A, Sethi A. A Dataset and a Technique for Generalized Nuclear Segmentation for Computational Pathology. IEEE Trans Med Imaging. 2017 Mar 6. doi. 10.1109/TMI.2017.2677499. [Epub ahead of print] PubMed PMID. 28287963.

2. Gough A, Stern AM, Maier J, Lezon T, Shun TY, Chennubhotla C, Schurdak ME, Haney SA, Taylor DL. Biologically Relevant Heterogeneity. Metrics and Practical Insights. SLAS Discov. 2017 Mar;22(3).213-237. doi. 10.1177/2472555216682725. PubMed PMID. 28231035.

3. Micolucci L, Rippo MR, Olivieri F, Procopio AD. Progress of research on microRNAs with diagnostic value in asbestos exposure. A call for method standardization. Biosci Trends. 2017 Jan 30. doi. 10.5582/bst.2016.01249. [Epub ahead of print] PubMed PMID. 28133000.

4. Rescigno T, Micolucci L, Tecce MF, Capasso A. Bioactive Nutrients and Nutrigenomics in Age-Related Diseases. Molecules. 2017 Jan 8;22(1). pii. E105. doi. 10.3390/molecules22010105. Review. PubMed PMID. 28075340.

5. Spagnolo DM, Gyanchandani R, Al-Kofahi Y, Stern AM, Lezon TR, Gough A, Meyer DE, Ginty F, Sarachan B, Fine J, Lee AV, Taylor DL, Chennubhotla SC. Pointwise mutual information quantifies intratumor heterogeneity in tissue sections labeled with multiple fluorescent biomarkers. J Pathol Inform. 2016 Nov 29;7.47. PubMed PMID. 27994939; PubMed Central PMCID. PMC5139455.

6. Ahern TP, Beck AH, Rosner BA, Glass B, Frieling G, Collins LC, Tamimi RM. Continuous measurement of breast tumour hormone receptor expression. a comparison of two computational pathology platforms. J Clin Pathol. 2016 Oct 11. pii. jclinpath-2016-204107. doi. 10.1136/jclinpath-2016-204107. [Epub ahead of print] PubMed PMID. 27729430.

7. Luo Y, Szolovits P, Dighe AS, Baron JM. Using Machine Learning to Predict Laboratory Test Results. Am J Clin Pathol. 2016 Jun;145(6).778-88. doi. 10.1093/ajcp/aqw064. PubMed PMID. 27329638.

8. Micolucci L, Akhtar MM, Olivieri F, Rippo MR, Procopio AD. Diagnostic value of microRNAs in asbestos exposure and malignant mesothelioma. systematic review and qualitative meta-analysis. Oncotarget. 2016 Sep 6;7(36).58606-58637. doi. 10.18632/oncotarget.9686. Review. PubMed PMID. 27259231; PubMed Central PMCID. PMC5295457.

9. Sethi A, Sha L, Vahadane AR, Deaton RJ, Kumar N, Macias V, Gann PH. Empirical comparison of color normalization methods for epithelial-stromal classification in H and E images. J Pathol Inform. 2016 Apr 11;7.17. doi. 10.4103/2153-3539.179984. PubMed PMID. 27141322; PubMed Central PMCID. PMC4837797.

10. García-Rojo M, Ordi J. Trying to Understand Digital Pathology before We Move to Computational Pathology. Pathobiology. 2016;83(2-3).57-60. doi. 10.1159/000443904. PubMed PMID. 27100520.

11. Ali HR, Dariush A, Provenzano E, Bardwell H, Abraham JE, Iddawela M, Vallier AL, Hiller L, Dunn JA, Bowden SJ, Hickish T, McAdam K, Houston S, Irwin MJ, Pharoah PD, Brenton JD, Walton NA, Earl HM, Caldas C. Computational pathology of pre-treatment biopsies identifies lymphocyte density as a predictor of response to neoadjuvant chemotherapy in breast cancer. Breast Cancer Res. 2016 Feb 16;18(1).21. doi. 10.1186/s13058-016-0682-8. PubMed PMID. 26882907; PubMed Central PMCID. PMC4755003.

12. Sarnecki JS, Burns KH, Wood LD, Waters KM, Hruban RH, Wirtz D, Wu PH. A robust nonlinear tissue-component discrimination method for computational pathology. Lab Invest. 2016 Apr;96(4).450-8. doi. 10.1038/labinvest.2015.162. PubMed PMID. 26779829; PubMed Central PMCID. PMC4808351.

13. Nawaz S, Yuan Y. Computational pathology. Exploring the spatial dimension of tumor ecology. Cancer Lett. 2016 Sep 28;380(1).296-303. doi. 10.1016/j.canlet.2015.11.018. PubMed PMID. 26592351.

14. Akhtar MM, Micolucci L, Islam MS, Olivieri F, Procopio AD. Bioinformatic tools for microRNA dissection. Nucleic Acids Res. 2016 Jan 8;44(1).24-44. doi. 10.1093/nar/gkv1221. Review. PubMed PMID. 26578605; PubMed Central PMCID. PMC4705652.

15. Ramamurthy B, Coffman FD, Cohen S. A perspective on digital and computational pathology. J Pathol Inform. 2015 Jun 3;6.29. doi. 10.4103/2153-3539.158059. PubMed PMID. 26110096; PubMed Central PMCID. PMC4470012.

16. Louis DN, Feldman M, Carter AB, Dighe AS, Pfeifer JD, Bry L, Almeida JS, Saltz J, Braun J, Tomaszewski JE, Gilbertson JR, Sinard JH, Gerber GK, Galli SJ, Golden JA, Becich MJ. Computational Pathology. A Path Ahead. Arch Pathol Lab Med. 2016 Jan;140(1).41-50. doi. 10.5858/arpa.2015-0093-SA. PubMed PMID. 26098131; PubMed Central PMCID. PMC4996078.

17. Tiwari S, Reddy VB, Bhargava R, Raman J. Computational chemical imaging for cardiovascular pathology. chemical microscopic imaging accurately determines cardiac transplant rejection. PLoS One. 2015 May 1;10(5).e0125183. doi. 10.1371/journal.pone.0125183. PubMed PMID. 25932912; PubMed Central PMCID. PMC4416885.

18. Roth KA, Almeida JS. Coming into focus. computational pathology as the new big data microscope. Am J Pathol. 2015 Mar;185(3).600-1. doi. 10.1016/j.ajpath.2015.01.002. PubMed PMID. 25701882.

19. Irshad H, Montaser-Kouhsari L, Waltz G, Bucur O, Nowak JA, Dong F, Knoblauch NW, Beck AH. Crowdsourcing image annotation for nucleus detection and segmentation in computational pathology. evaluating experts, automated methods, and the crowd. Pac Symp Biocomput. 2015.294-305. PubMed PMID. 25592590; PubMed Central PMCID. PMC4299942.

20. Dong F, Irshad H, Oh EY, Lerwill MF, Brachtel EF, Jones NC, Knoblauch NW, Montaser-Kouhsari L, Johnson NB, Rao LK, Faulkner-Jones B, Wilbur DC, Schnitt SJ, Beck AH. Computational pathology to discriminate benign from malignant intraductal proliferations of the breast. PLoS One. 2014 Dec 9;9(12).e114885. doi. 10.1371/journal.pone.0114885. PubMed PMID. 25490766; PubMed Central PMCID. PMC4260962.

21. Louis DN, Gerber GK, Baron JM, Bry L, Dighe AS, Getz G, Higgins JM, Kuo FC, Lane WJ, Michaelson JS, Le LP, Mermel CH, Gilbertson JR, Golden JA. Computational pathology. an emerging definition. Arch Pathol Lab Med. 2014 Sep;138(9).1133-8. doi. 10.5858/arpa.2014-0034-ED. PubMed PMID. 25171694.

22. Schüffler PJ, Fuchs TJ, Ong CS, Wild PJ, Rupp NJ, Buhmann JM. TMARKER. A free software toolkit for histopathological cell counting and staining estimation. J Pathol Inform. 2013 Mar 30;4(Suppl).S2. doi. 10.4103/2153-3539.109804. PubMed PMID. 23766938; PubMed Central PMCID. PMC3678753.

23. Fuchs TJ, Buhmann JM. Computational pathology. challenges and promises for tissue analysis. Comput Med Imaging Graph. 2011 Oct-Dec;35(7-8).515-30. doi. 10.1016/j.compmedimag.2011.02.006. PubMed PMID. 21481567.

24. Floros X, Fuchs TJ, Rechsteiner MP, Spinas G, Moch H, Buhmann JM. Graph-based pancreatic islet segmentation for early type 2 diabetes mellitus on histopathological tissue. Med Image Comput Comput Assist Interv. 2009;12(Pt 2).633-40. PubMed PMID. 20426165.

25. Fuchs TJ, Wild PJ, Moch H, Buhmann JM. Computational pathology analysis of tissue microarrays predicts survival of renal clear cell carcinoma patients. Med Image Comput Comput Assist Interv. 2008;11(Pt 2).1-8. PubMed PMID. 18982583.

[ArtPoon]

Moving issue to another repo