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| Open Knee(s) project will generate a plethora of heterogeneous data sets, e.g. DICOM images, joint/tissue mechanical testing data, etc. It is unnecessary and sometimes clumsy to put the data into source code repositories. The workflow of the "Downloads" section at the project site also seems cumbersome for intermediate storage of data, which may not be release ready. This specification is targeted to find a solution for online storage of data (in-house or at Open Knee(s) project site) that will accommodate the workflow of data collection, analysis, and public release. A separate project site at SimTK.org is available to expand management of data and relevant information for biomechanics studies beyond the realm of Open Knee(s), see https://simtk.org/home/dmmb. | Open Knee(s) project will generate a plethora of heterogeneous data sets, e.g. DICOM images, joint/tissue mechanical testing data, etc. It is unnecessary and sometimes clumsy to put the data into source code repositories. The workflow of the "Downloads" section at the project site also seems cumbersome for intermediate storage of data, which may not be release ready. This specification is targeted to find a solution for online curation and storage of data (in-house or at Open Knee(s) project site) that will accommodate the workflow of data collection, analysis, and public release. A separate project site at SimTK.org is available to expand management of data and relevant information for biomechanics studies beyond the realm of Open Knee(s), see https://simtk.org/home/dmmb. |
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| Storage of data for future discoverability, retrieval, and dissemination | Curation and storage of specimen/sample associated data for discoverability, retrieval, and dissemination |
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| * A data management system, e.g. [http://www.midasplatform.org/ Midas Platform]. | == Infrastructure == * A data management system, e.g. [http://www.midasplatform.org/ Midas Platform], for data curation. * A dissemination platform, e.g. Downloads section of [https://simtk.org/home/openknee], also see ["Infrastructure/Collaboration"] |
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* ["Specifications/Specimens"] * ["Specifications/SpecimenPreparation"] == Related Protocols == |
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| == Input == | == Specimen/Sample Labeling == |
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| == Procedures == | === Joint === |
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| -- ["aerdemir"] [[DateTime(2014-02-11T13:05:40Z)]] This section may list general purpose procedures and alternatives to utilize the same input to reach the same output. Procedures optimized for specific experimentation protocols should also be provided in here. | Whole knee specimen labels include the Open Knee(s) abbreviation in lower case, oks, immediately followed by three numerals to indicate specimen number, e.g. 001. An example for knee specimen labeling is in following: |
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| === Labeling conventions === | oks001:: Open Knee(s) Specimen 1 |
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| ==== Tissue samples and data ==== | === Tissue === |
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| ===== Proposed tissue sample and data labeling convetion ===== | Tissue testing plans of Open Knee(s) will require a large set of tissue samples acquired from a single knee specimen; see details in ["Specifications/SpecimenPreparation"] and ["Specifications/ExperimentationTissueMechanics"]. For example, confined and unconfined compression testing of cartilage will require a total of 10 samples from medial and lateral sides of femur and tibia, and from patella. Compression and tension testing of menisci will require a total of 4 samples from medial and lateral sides. Uniaxial tension testing of ligaments and tendons will require a total of 6 samples from their midsubstance (cruciate, collateral, and patellar ligaments, quadriceps tendon). For a single knee, a total of 20 tissue samples may need to acquired, indicating a need for organization of samples and accompanying data. |
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| Labels for tissue samples include knee specimen label, e.g. oks002, followed by three letter tissue type in upper case, e.g. TBC, four letter tissue location in upper case (from gross to granular location, lower case if at microscale), and two numerals to indicate sample number. When needed, the character ''X'' is used as a filler. A few examples for tissue samples are in following: | |
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| 1. Expected samples: | oks001-PTC-MCXX-02:: sample 2 from patellar cartilage of Open Knee(s) Specimen 1, acquired from the medial side at the center. oks002-MNS-MAvX-01:: sample 1 from medial meniscus of Open Knee(s) Specimen 2, acquired from middle layer of the tissue at the anterior side. |
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| * Cartilage * Test type: Confined compression * Sample location: * Femur, medial * Femur, lateral * Tibia, medial * Tibia, lateral * Patella * Meniscus * Test type: Confined compression, Uniaxial tension * Sample location: * medial * lateral * Ligaments (Anetrior and posterior cruciate ligaments, medial and lateral collateral ligaments, and patellar ligament) * Test type: Uniaxial tension * Sample location: Mid-substance * Tendon (Quadricep) * Test type: Uniaxial tension * Sample location: Mid-substance |
==== Tissue Types ==== |
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| 2. Minimum number of samples: 15 | * Bone * '''FMB''': femur * '''TBB''': tibia * '''FBB''': fibula * '''PTB''': patella * Cartilage * '''FMC''': femoral cartilage * '''TBC''': tibial cartilage * '''PTC''': patellar cartilage * Meniscus * '''MNS''': meniscus * Ligament * '''ACL''': anterior cruciate ligament * '''PCL''': posterior cruciate ligament * '''MCL''': medial collateral ligament * '''LCL''': lateral collateral ligament * '''PTL''': patellar ligament * Tendon * '''QAT''': quadriceps tendon |
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| * Compression: 7 (1 patella, 4 cartilage, 2 meniscus) * Tension: 8 (5 ligaments, 2 meniscus, 1 tendon) |
==== Tissue Locations ==== |
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| 3. Tissue Sample/data labels: | The tissue location is labeled starting from its gross location and ending with its granular position. |
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| Note: Trial number will appear only for data files. | * Bone * '''M''' or '''L''': medial or lateral * '''A''' or '''P''': anterior or posterior * '''S''' or '''I''': superior or inferior * '''C''': central * Cartilage * '''M''' or '''L''': medial or lateral * '''A''' or '''P''': anterior or posterior * '''C''': central * '''u''' or '''v''' or '''w''': superficial or transitional or deep zone * Meniscus * '''M''' or '''L''': medial or lateral * '''A''' or '''P''': anterior or posterior * '''C''': central * '''u''' or '''v''' or '''w''': femur side or mid-substance or tibia side * Ligament * '''S''' or '''I''' or '''C''': superior or inferior or central * Tendon * '''S''' or '''I''' or '''C''': superior or inferior or central |
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| Examples (only tissue type and tissue location are shown): | |
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| Labeling convention: specimen identifier - tissue type and orientation/ location identifier - test type identifier - trial number/ sample number identifier | FMC-MAXX:: femoral cartilage sample acquired medially and anteriorly TBC-LAuX:: tibial cartilage sample acquired laterally and anteriorly from the superficial zone FMC-AXXX:: femoral cartilage sample acquired from the trochlear groove MNS-LCwX:: sample acquired from lateral meniscus centrally and from mid-substance MCL-IXXX:: medial collateral ligament sample acquired from inferior region |
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| * Cartilage: * OK_ _-FECM-_-_ _ (medial femoral cartilage) * OK_ _-FECL-_-_ _ (lateral femoral cartilage) * OK_ _-PAC_-_-_ _ (Patellar cartilage) * OK_ _-TICM-_-_ _(medial tibial cartilage) * OK_ _-TICL-_-_ _(lateral tibial cartilage) |
attachment:t_loc-labels.png |
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* Meniscus: * OK_ _-MME(A/P/M)-_-_ _ (Location identifiers : A (anterior), P (posterior), M (middle)) * OK_ _-LME(A/P/M)-_-_ _ * Tendon: * OK_ _-QAT(S/M/I)-_-_ _ (Location identifiers : S (Superior), M (mid-substance), M (Inferior)) attachment:tissue_label.txt == Output == |
== Data Labeling == |
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== Data Curation == '''Note:''' Trial number will appear only for data files. == Data Dissemination == |
Overview
Open Knee(s) project will generate a plethora of heterogeneous data sets, e.g. DICOM images, joint/tissue mechanical testing data, etc. It is unnecessary and sometimes clumsy to put the data into source code repositories. The workflow of the "Downloads" section at the project site also seems cumbersome for intermediate storage of data, which may not be release ready. This specification is targeted to find a solution for online curation and storage of data (in-house or at Open Knee(s) project site) that will accommodate the workflow of data collection, analysis, and public release. A separate project site at SimTK.org is available to expand management of data and relevant information for biomechanics studies beyond the realm of Open Knee(s), see https://simtk.org/home/dmmb.
Target Outcome
Curation and storage of specimen/sample associated data for discoverability, retrieval, and dissemination
Prerequisites
Infrastructure
A data management system, e.g. [http://www.midasplatform.org/ Midas Platform], for data curation.
A dissemination platform, e.g. Downloads section of [https://simtk.org/home/openknee], also see ["Infrastructure/Collaboration"]
Previous Protocols
- ["Specifications/Specimens"]
- ["Specifications/SpecimenPreparation"]
Related Protocols
Any experimentation protocol, see
- ["Specifications/ExperimentationAnatomicalImaging"]
- ["Specifications/ExperimentationJointMechanics"]
- ["Specifications/ExperimentationTissueMechanics"]
Protocols
Specimen/Sample Labeling
Joint
Whole knee specimen labels include the Open Knee(s) abbreviation in lower case, oks, immediately followed by three numerals to indicate specimen number, e.g. 001. An example for knee specimen labeling is in following:
- oks001
- Open Knee(s) Specimen 1
Tissue
Tissue testing plans of Open Knee(s) will require a large set of tissue samples acquired from a single knee specimen; see details in ["Specifications/SpecimenPreparation"] and ["Specifications/ExperimentationTissueMechanics"]. For example, confined and unconfined compression testing of cartilage will require a total of 10 samples from medial and lateral sides of femur and tibia, and from patella. Compression and tension testing of menisci will require a total of 4 samples from medial and lateral sides. Uniaxial tension testing of ligaments and tendons will require a total of 6 samples from their midsubstance (cruciate, collateral, and patellar ligaments, quadriceps tendon). For a single knee, a total of 20 tissue samples may need to acquired, indicating a need for organization of samples and accompanying data.
Labels for tissue samples include knee specimen label, e.g. oks002, followed by three letter tissue type in upper case, e.g. TBC, four letter tissue location in upper case (from gross to granular location, lower case if at microscale), and two numerals to indicate sample number. When needed, the character X is used as a filler. A few examples for tissue samples are in following:
- oks001-PTC-MCXX-02
- sample 2 from patellar cartilage of Open Knee(s) Specimen 1, acquired from the medial side at the center.
- oks002-MNS-MAvX-01
- sample 1 from medial meniscus of Open Knee(s) Specimen 2, acquired from middle layer of the tissue at the anterior side.
Tissue Types
- Bone
FMB: femur
TBB: tibia
FBB: fibula
PTB: patella
- Cartilage
FMC: femoral cartilage
TBC: tibial cartilage
PTC: patellar cartilage
- Meniscus
MNS: meniscus
- Ligament
ACL: anterior cruciate ligament
PCL: posterior cruciate ligament
MCL: medial collateral ligament
LCL: lateral collateral ligament
PTL: patellar ligament
- Tendon
QAT: quadriceps tendon
Tissue Locations
The tissue location is labeled starting from its gross location and ending with its granular position.
- Bone
M or L: medial or lateral
A or P: anterior or posterior
S or I: superior or inferior
C: central
- Cartilage
M or L: medial or lateral
A or P: anterior or posterior
C: central
u or v or w: superficial or transitional or deep zone
- Meniscus
M or L: medial or lateral
A or P: anterior or posterior
C: central
u or v or w: femur side or mid-substance or tibia side
- Ligament
S or I or C: superior or inferior or central
- Tendon
S or I or C: superior or inferior or central
Examples (only tissue type and tissue location are shown):
- FMC-MAXX
- femoral cartilage sample acquired medially and anteriorly
- TBC-LAuX
- tibial cartilage sample acquired laterally and anteriorly from the superficial zone
- FMC-AXXX
- femoral cartilage sample acquired from the trochlear groove
- MNS-LCwX
- sample acquired from lateral meniscus centrally and from mid-substance
- MCL-IXXX
- medial collateral ligament sample acquired from inferior region
attachment:t_loc-labels.png
Data Labeling
- Online storage of annotated data for prospective
- discoverability (for internal use)
- retrieval (for internal use),
- and dissemination (through Open Knee(s) site at SimTK.org)
Data Curation
Note: Trial number will appear only for data files.