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Expressing Medical Image Measurements Using Ontologies from the OBO Library

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Expressing Medical Image Measurements Using Ontologies from the OBO Library CrEDIBLE Thematic Working Days / October 8-10, 2014 Expressing Medical Image Measurements using Ontologies from the OBO Library Heiner Oberkampf1,2, James A. Overton3, Sonja Zillner1, Bernhard Bauer2 and Matthias Hammon4 1Siemens AG, Corporate Technology 2University of Augsburg, Software Methodologies for Distributed Systems 3Knocean 3University Hospital Erlangen, Department of Radiology Unrestricted © Siemens AG 2014. All rights reserved Agenda Measurements in Radiology and Pathology Expressing Measurements Normal Size Specifications Applications Page 2 October 2014 Corporate Technology Unrestricted © Siemens AG 2014. All rights reserved Measurements in Radiology Not comprehensive list 1) Size length: 1D, 2D, 3D area, volume index (e.g. spleen index = width*height*depth) Density measured in Hounsfield scale (Hu) mainly in CT images minimal, maximal and mean density values for Regions of Interest (ROIs) Angle e.g. bone configurations or fractions Blood flow e.g. PET: myocardial blood flow and blood flow in brain … 1) Source: http://www.recist.com/recist-in-practice/19.html Page 3 October 2014 Corporate Technology Unrestricted © Siemens AG 2014. All rights reserved Measurements in Pathology Not comprehensive Size length: 1D, 2D, 3D area, volume Weight weight of resected tissue, nodule or tumor Ratios immunohistochemical staining of tumor cells Other measurements viscosity of blood, serum, and plasma mitotic rate serum concentration … Page 4 October 2014 Corporate Technology Unrestricted © Siemens AG 2014. All rights reserved Longitudinal Integration Image source: “Automated Detection and Volumetric Segmentation of the Spleen in CT Scans” M. Hammon, P. Dankerl, M. Kramer, S. Seifert, A. Tsymbal2, M. J. Costa2, R. Janka1, M. Uder1, A. Cavallaro Page 5 October 2014 Corporate Technology Unrestricted © Siemens AG 2014. All rights reserved Agenda Measurements in Radiology and Pathology Expressing Measurements Normal Size Specifications Applications Page 6 October 2014 Corporate Technology Unrestricted © Siemens AG 2014. All rights reserved Reused Ontologies The following ontologies are used to express measurement information. Basic Formal Ontology (BFO2) Completely domain independent Relations Ontology (RO) has_part, has_participant, located_in … Information Artifact Ontology (IAO) document, report, figure, measurement datum ... Integration and extensions Ontology for Biomedical Investigations (OBI) Model for Clinical value specification, study, tissue specimen, plan, prediction, staining, … Information (MCI) Phenotypic Quality (PATO) size, length, diameter, mass, color … Units Ontology (UO) units for length, mass and time. Biological Spatial Ontology (BSPO) anatomical axis, anatomical plane, … Used Reference Terminologies: Ontology for General Medical Science (OGMS) • Foundational Model of Anatomy (FMA) basic clinical concepts like, e.g., diagnosis, clinical finding, pathological anatomical structure … • Radiological Lexicon (RadLex) Page 7 October 2014 Corporate Technology Unrestricted © Siemens AG 2014. All rights reserved obi:value specification The element "1.8 cm" can occur in many different parts of a biomedical investigation. “1.8 cm” might be part of: • the data resulting from a measurement of one of John's lymph nodes, made on January 12, 2014 in Berlin • a protocol, i.e. a specification of a plan to make some measurement • a prediction of the result a measurement planned for the future • a rule for classifying measurements • many more … OBI uses the "value specification" approach to capture the shared structure across different uses and allow for easy comparison between them. Page 8 October 2014 Corporate Technology Unrestricted © Siemens AG 2014. All rights reserved obi:value specification Shared Structure in Different Contexts Definition: An information content entity that specifies a value within a classification scheme or on a quantitative scale. Example of usage: The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass. uo:unit iao:has measurement unit label some particular obi:has value obi:value measurement datum, specification specification prediction, etc. obi:has specified value xsd:float, xsd:int, … Page 9 October 2014 Corporate Technology Unrestricted © Siemens AG 2014. All rights reserved Length Measurements Example: Lymph node with diameter 1.8 cm. ogms:clinical finding radlex:lymph node _:cf iao:is about _:ln ro:has_part pato:size pato:length bfo:inheres in pato:diameter iao:length measurement datum _:diam-ln iao:is quality measurement of _:md obi:scalar value specification uo:length unit obi:has value specification iao:has measurement unit label uo:centimeter _:vs obi:has specified value “1.8”^^xsd:float Page 10 October 2014 Corporate Technology Unrestricted © Siemens AG 2014. All rights reserved Length Measurements Example: Width of kidney 5.2 cm. ogms:clinical finding radlex:kidney _:cf iao:is about _:kidney pato:size ro:has_part pato:width bfo:inheres in bspo:sagittal plane iao:length measurement datum _:kidneyw mci:orthogonal_to _:sp iao:is quality measurement of _:md obi:scalar value specification uo:length unit obi:has value specification iao:has measurement unit label uo:centimeter _:vs obi:has specified value “5.2”^^xsd:float Page 11 October 2014 Corporate Technology Unrestricted © Siemens AG 2014. All rights reserved Length Measurements Example: Width of kidney 5.2 cm. ogms:clinical finding radlex:kidney _:cf iao:is about _:kidney pato:size ro:has_part pato:width bfo:inheres in iao:length bspo:left-right axis measurement datum iao:is quality _:kidneyw measurement of _:md obi:scalar value specification uo:length unit obi:has value specification iao:has measurement unit label uo:centimeter _:vs obi:has specified value “1.8”^^xsd:float Page 12 October 2014 Corporate Technology Unrestricted © Siemens AG 2014. All rights reserved 2D Measurements Example with RECIST RECIST (Response Evaluation Criteria In Solid Tumors) “First you need to identify the longest [in plane] diameter of a lymph node or nodal mass (here 56.0mm) and then choose the longest perpendicular diameter to that as the short axis (here 45.3mm).” Source: http://www.recist.com/recist-in-practice/19.html Page 13 October 2014 Corporate Technology Unrestricted © Siemens AG 2014. All rights reserved 2D Measurements Example: Lymph node with diameter 56.0 x 45.3 mm. ogms:clinical finding mci:two directional radlex:lymph node size finding _:cf iao:is about _:ln bspo:transverse plane bfo:inheres_in ro:has_part mci:longest _:tp diameter mci:short axis iao:length mci:axis measurement datum within plane _:longest-diam _:diam-short-axis _:md iao:is quality measurement of mci:orthogonal to _:md2 obi:scalar value uo:length unit specification obi:has value specification uo:centimeter _:vs obi:has “5.6”^^xsd:float _:vs2 specified value “4.53”^^xsd:float Page 14 October 2014 Corporate Technology Unrestricted © Siemens AG 2014. All rights reserved Density Measurements Density is measured in Hounsfield unit (HU) Density measurements given for a region of interest (ROI) Minimal, maximal and mean values for the pixels of the ROI Examples: “Density of a liver cyst 8 HU” Density measurement of a liver cyst Page 15 October 2014 Corporate Technology Unrestricted © Siemens AG 2014. All rights reserved Image Regions Image regions are not defined in existing ontologies of the OBO Library. Definitions: An image region is a data item representing a subset of pixels of some image. A region of interest is an image region identified for a particular purpose. Related Work: The Open Microscopy Environment (OME) www.openmicroscopy.org Page 16 October 2014 Corporate Technology Unrestricted © Siemens AG 2014. All rights reserved Region of Interest iao:image :img mci:image region mci:geometrical shape ro:is contained in mci:region of interest mci:ellipse :e mci:specified by :roi Page 17 October 2014 Corporate Technology Unrestricted © Siemens AG 2014. All rights reserved Density Measurement iao:image ogms:clinical finding :img mci:documented in _:cf ro:has_part ro:is iao:measurement contained in datum pato:mass density obi:average :geometrical shape :region of interest value _:density :ellipse iao:is quality measurement of _:roi _:avmd obi:scalar value mci:specified by ro:derives obi:has value specification _:e from specification radlex:Houndsfield unit iao:has measurement unit _:vs label obi:has “8.0”^^xsd:float specified value Page 18 October 2014 Corporate Technology Unrestricted © Siemens AG 2014. All rights reserved Ratio Measurements Percentage of Ki-67 positive tumor cells Ki-67 is a protein in cells that increases as they prepare to divide into new cells. A staining process can measure the percentage of tumor cells that are positive for Ki-67. The more positive cells there are, the more quickly they are dividing and forming new cells. In breast cancer, a result of less than 10% is considered low, 10-20% is intermediate/borderline, and more than 20% is considered high. Ki-67 immunostaining of brain tumor cells Image Source: Wikipedia Page 19 October 2014 Corporate Technology Unrestricted © Siemens AG 2014. All rights reserved Representation of Ratio Measurements Work-in-progress pato:quality mci:prevalence of Ki-67 positive cells in a tumor :tumor iao:scalar measurement datum :prevOfKi67 bfo:inheres in _:tumor iao:is quality measurement of :Ki-67+ cell ratio specification obi:scalar value uo:ratio obi:has value specification specification iao:has measurement uo:percent _:svs unit label obi:has
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