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= Target Outcome = | = Target Outcome =http://wiki.simtk.org/cpms/ |
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* '''~+oks001+~''' | oks001:: Open Knee(s) Specimen 1 |
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* '''~+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. |
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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'''Tissue Types''' | ==== Tissue Types ==== |
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'''Tissue Locations''' | * 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 === |
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 =http://wiki.simtk.org/cpms/
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
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, 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 ===
1. Expected samples:
- 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
2. Minimum number of samples: 16
- Compression: 8 (1 patella, 1 trochlear groove, 4 cartilage, 2 meniscus)
- Tension: 8 (5 ligaments, 2 meniscus, 1 tendon)
3. Tissue Sample/data labels:
Note: Trial number will appear only for data files.
Labeling convention: specimen identifier - tissue type identifier - location identifier (1 character for each direction. e.g MA= medial anterior) - trial number/ sample number identifier
- Cartilage:
- OK_ _-FMC-MXXX-_ _ (medial femoral cartilage)
- OK_ _-FMC-LXXX-_ _ (lateral femoral cartilage)
- OK_ _-FMC-AXXX-_ _ (Trochlear groove)
- OK_ _-PTC-MXXX-_ _ (Patellar cartilage)
- OK_ _-TBC-MXXX-_ _(medial tibial cartilage)
- OK_ _-TBC-LXXX-_ _(lateral tibial cartilage)
Note: Depth identifiers: u = superficial layer, v=middle layer, w=deep layer
- Meniscus:
- OK_ _-MNS-(MAXX/MPXX/MCXX)-_ _ (Location identifiers : A (anterior), P (posterior), C (center))
- OK_ _-MNS-(LAXX/LPXX/LCXX)-_ _
- Tendon:
- OK_ _-QAT-(SXXX/CXXX/IXXX)-_ _ (Location identifiers : S (Superior), C (center/ mid-substance), I (Inferior))
- Ligaments:
- OK_ _-ACL-(SXXX/CXXX/IXXX)-_ _ (Location identifiers : S (Superior), C (center/mid-substance), I (Inferior))
- OK_ _-PCL-(SXXX/CXXX/IXXX)-_ _
- OK_ _-MCL-(SXXX/CXXX/IXXX)-_ _
- OK_ _-LCL-(SXXX/CXXX/IXXX)-_ _
- OK_ _-PTL-(SXXX/CXXX/IXXX)-_ _
attachment:t_loc-labels.png
- attachment:tissue_label.txt
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