From dec29376edfc1a1ed8be0b13815b239ec2efe951 Mon Sep 17 00:00:00 2001 From: ty-esi Date: Wed, 29 Oct 2025 14:22:44 -0500 Subject: [PATCH 1/2] add ICDC static files --- model-desc/Data_Model_Navigator_README.md | 49 +++++++ model-desc/Icon-DMNav.85x85.svg | 124 ++++++++++++++++++ ...fer_Manifest - Sequence Analysis Files.tsv | 93 +++++++++++++ ...1-File_Transfer_Manifest - Study Files.tsv | 4 + .../TCL01-case.txt | 46 +++++++ .../TCL01-demographic.txt | 46 +++++++ .../TCL01-diagnosis.txt | 46 +++++++ .../TCL01-enrollment.txt | 46 +++++++ .../TCL01-principal_investigator.txt | 2 + .../TCL01-publication.txt | 2 + .../TCL01-sample.txt | 47 +++++++ .../TCL01-study.txt | 2 + 12 files changed, 507 insertions(+) create mode 100644 model-desc/Data_Model_Navigator_README.md create mode 100644 model-desc/Icon-DMNav.85x85.svg create mode 100644 model-desc/TCL01 Loading File Example Set/TCL01-File_Transfer_Manifest - Sequence Analysis Files.tsv create mode 100644 model-desc/TCL01 Loading File Example Set/TCL01-File_Transfer_Manifest - Study Files.tsv create mode 100644 model-desc/TCL01 Loading File Example Set/TCL01-case.txt create mode 100644 model-desc/TCL01 Loading File Example Set/TCL01-demographic.txt create mode 100644 model-desc/TCL01 Loading File Example Set/TCL01-diagnosis.txt create mode 100644 model-desc/TCL01 Loading File Example Set/TCL01-enrollment.txt create mode 100644 model-desc/TCL01 Loading File Example Set/TCL01-principal_investigator.txt create mode 100644 model-desc/TCL01 Loading File Example Set/TCL01-publication.txt create mode 100644 model-desc/TCL01 Loading File Example Set/TCL01-sample.txt create mode 100644 model-desc/TCL01 Loading File Example Set/TCL01-study.txt diff --git a/model-desc/Data_Model_Navigator_README.md b/model-desc/Data_Model_Navigator_README.md new file mode 100644 index 0000000..f0dae39 --- /dev/null +++ b/model-desc/Data_Model_Navigator_README.md @@ -0,0 +1,49 @@ +### The Graph-Based Data Model +The ICDC data model is graph-based, where nodes are functionally equivalent to the tables of a traditional relational database, and the properties within each node effectively represent what would be columns or fields in the corresponding table, with relationships stored at the level of individual records. More importantly, however, the data model was developed to support both cross-sectional studies aimed at answering questions concerning basic cancer biology and the mechanisms by which malignancies develop, and longitudinal clinical trials assessing therapeutic interventions in canine subjects who have developed spontaneous cancers. Accordingly, although no single study is likely to propagate data into every node, let alone every property within every node, the data model has sufficient inherent flexibility to accommodate any given type of canine study. + + +### Node Categories +All nodes are assigned to one of several categories, with each category representing a family of inter-related nodes which collectively define the various higher-level entities within the data model. For example, the **Case** category defines a small group of nodes which fully characterize ICDC’s cases/subjects/donors and the **Study** category contains the nodes which collectively define the various aspects of studies, whereas the larger **Clinical Trial** category groups together the nodes within which data from various types of clinical trial observations can be represented. + + +### Assignment: Core nodes versus Extended nodes +As data on-boarding has progressed, there are a number of nodes which are always or least very frequently populated with data regardless of the type of study, and such nodes, which are at the very center, i.e. ***core***, of the data model, are therefore classified as “Core” nodes. Beyond the core data model lies the extended data model, which contains numerous nodes which are currently less densely populated, most notably the Clinical Trial nodes described above. Dividing the data model into these two spheres is intended to help focus the attention of users, particularly data submitters, upon the nodes and properties most critical to the definition of any given study, regardless of its nature. + + +### Class: Primary nodes versus Secondary nodes +Within the delineation of the core data model from its extended counterpart, there are nodes which are more important and therefore more densely populated, i.e. nodes designated as “Primary” nodes, versus those that are less important and/or less densely populated, i.e. nodes designated as “Secondary” nodes. Nodes designated as both “Core” and “Primary” will contain numerous required properties, and effectively represent required nodes which form the ***backbone*** of any given study. In contrast, nodes that are designated as “Core” and “Secondary” can be thought of as optional nodes, even though they may contain required fields. These secondary nodes house valuable accessory data, which is relevant to and/or generated by some studies, but by no means all. + + +### Facet-Based Filtering +The facet-based filtering options presented within the left-hand sidebar of the Data Model Navigator allow users to filter the display of nodes based upon their designations for Category, Assignment and Class; based upon nodes containing required versus preferred versus optional properties; and based upon nodes containing properties that are displayed within the application’s user interface (UI). Using this array of filtering criteria, users can quickly partition the data model into smaller sets of nodes and thereby identify nodes of particular interest. Note that filtering criteria can be applied to both the Graph View and the Table View, and that filter selections are maintained when switching back and forth between viewing modes. + + +### Graph View +In Graph View mode, the Data Model Navigator provides users with an interactive, graphical rendering of the data model, which can be filtered as described above, in order to identify the nodes and therefore properties of most relevance or interest. Selecting a node of interest invokes a Properties Dialogue box which indicates the node’s Assignment and Class designations and quantifies the number of properties within the node that are Required, Preferred and Optional. A detailed tabular view of the node can be invoked by selecting the “Open Properties” option displayed within the Properties Dialogue box. + + +### Table View +In Table View mode, the Data Model Navigator displays detailed tabular views of each node, which fully-define the properties within them, inclusive of the applicable controlled vocabularies of acceptable terms for enumerated properties. The tabular views also clearly identify which properties are Required versus those that are Preferred or Optional; the acceptable data type for each property; which properties are displayed within the application’s UI; and the labels via which such properties are displayed. Note that many properties displayed within the UI are renamed with labels which are more intuitive than the property names themselves, and that some properties are displayed via more than one label. As described below, comprehensive documentation of the data model’s nodes and property requirements can be downloaded in PDF format via the Table View, alongside node-specific data loading templates into which data submitters can insert the relevant data values and thereby create loading-ready data files. + + +### Required, Preferred and Optional Properties +Each property is assigned one of three requirement levels - Required, Preferred, or Optional. +* **Required** properties are largely self-explanatory, i.e. data destined for a node which contains required properties must include values for all such properties, and values must be compliant with the acceptable values for properties which are both required and enumerated. Controlled vocabularies for such properties typically include terms such as “Not Applicable”, “Not Determined” and “Unknown” to accommodate situations where data values aren’t relevant or weren’t collected, either by design or otherwise. Notably, for nodes into which a data submitter is not propagating any data values, required fields are no longer relevant, and can be ignored. +* **Preferred** properties represent properties for which data values are not required, but which add significant insight and detail, have been populated to a significant degree thus far, and for which data is typically available when requested during study on-boarding. + +* **Optional** properties are precisely that and null values are allowed. + +### Key Properties +Many nodes contain a single property visually identified as a Key Property by a **blue key icon** displayed next to the name of the appropriate property. In addition to several nodes that require one in support of data updates, all nodes which act as parents of child nodes will likewise have a single property within them identified as a Key Property. During data loading, ***child records*** are associated with their correct ***parents*** by virtue of data loading files which contain the appropriate values for the property identified as their parents’ Key Property. For example, files via which sample records are loaded will contain a column into which values of “Case ID” must be inserted, such that samples can be associated with the appropriate case from which they were derived, with “Case ID” being designated as the Key Property within the **Case** node. Key Properties are therefore functionally equivalent to foreign keys in traditional relational databases. + + +### PDF Documentation +Detailed documentation of the data model’s nodes and property requirements can be downloaded as PDF exports, either in the form of a comprehensive data dictionary inclusive of all nodes, invoked via the upper-level “Available Downloads” option, or from within the Table View, and invoked on a node-by-node basis. Used alongside the corresponding data loading templates described below, these node-specific PDF exports function as user guides for data preparation and submission. See the associated [Data Submission Guidelines](/#/submit) + + +### Data Loading Templates +In support of data submission, data loading templates can be downloaded, either in the form of a zip file containing copies of all available templates, invoked via the upper-level “Available Downloads” option, or from within the Table View, and invoked on a node-by-node basis. Templates include columns into which the data values required to associate child records with their parents can be inserted. Notably, each template will include a **mapping column** for each potential parent, but although *all child records must be mapped to **at least one parent***, submitters are not required to provide a mapping value for each and every potential parent, *only the* ***most appropriate parent(s)***. Guided by the corresponding node-specific PDF exports described above, data submitters can insert the relevant data values into these data loading templates, and thereby create loading-ready data files that can be handed off to the ICDC Data Team. + + +### Controlled Vocabularies +In the interests of data quality and consistency, the ICDC data model makes extensive use of enumerated properties and controlled vocabularies of acceptable terms. All such controlled vocabularies can be viewed via Table View mode, and value sets are included in full in the appropriate PDF exports. Furthermore, in support of data submitters pre-validating their templated data, all controlled vocabularies can be exported in machine readable JSON and TSV formats, either in the form of a zip file containing copies of controlled vocabularies for all enumerated properties, invoked via the upper-level “Available Downloads” option, or from within the Table View, and invoked on a property-by-property basis. As more studies are added to the ICDC, many of these controlled vocabularies will continue to evolve, and will be updated by the ICDC Data Team during study on-boarding, in order to accommodate additional terms not yet encountered. diff --git a/model-desc/Icon-DMNav.85x85.svg b/model-desc/Icon-DMNav.85x85.svg new file mode 100644 index 0000000..57907c2 --- /dev/null +++ b/model-desc/Icon-DMNav.85x85.svg @@ -0,0 +1,124 @@ + + + + + + + + + + + + + + + + + + + + + + diff --git a/model-desc/TCL01 Loading File Example Set/TCL01-File_Transfer_Manifest - Sequence Analysis Files.tsv b/model-desc/TCL01 Loading File Example Set/TCL01-File_Transfer_Manifest - Sequence Analysis Files.tsv new file mode 100644 index 0000000..6af23b6 --- /dev/null +++ b/model-desc/TCL01 Loading File Example Set/TCL01-File_Transfer_Manifest - Sequence Analysis Files.tsv @@ -0,0 +1,93 @@ +type sample.sample_id file_name file_type file_description original_file_size original_md5sum +file TCL01-17-71 1771_recal_reads.bai Index File tumor cell line sample, TCL01-17-71: bam index of WES reads 6193232 09ed1edc79ec99b73833b08833ee401f +file TCL01-17-71 1771_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-17-71: WES reads to CanFam3.1 15575029136 8bafe042b0763e32b45ba2c0b9b080fe +file TCL01-17CM98 17CM98_recal_reads.bai Index File tumor cell line sample, TCL01-17CM98: bam index of WES reads 6154544 9c3b9c02db8d16dc0796e77ec36c802b +file TCL01-17CM98 17CM98_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-17CM98: WES reads to CanFam3.1 15935376497 c480c22d6eb7560b1e406767fc7069bb +file TCL01-Abrams ABRAMS_recal_reads.bai Index File tumor cell line sample, TCL01-Abrams: bam index of WES reads 6129784 7eaac5b155f96e16af9545e456244e29 +file TCL01-Abrams ABRAMS_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-Abrams: WES reads to CanFam3.1 14521128290 679600426205d8a7bf5e98cf26a4e6b1 +file TCL01-Angus ANGUS_recal_reads.bai Index File tumor cell line sample, TCL01-Angus: bam index of WES reads 6007608 cd8d7f8babd7c827acf63809c6000b83 +file TCL01-Angus ANGUS_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-Angus: WES reads to CanFam3.1 12309776649 a91d206c8d7612143f350d03f559a717 +file TCL01-Bliley BLILEY_recal_reads.bai Index File tumor cell line sample, TCL01-Bliley: bam index of WES reads 6190512 083f20373c0274ce6908276abb980360 +file TCL01-Bliley BLILEY_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-Bliley: WES reads to CanFam3.1 12379230451 eb7fb184c629ef4a7cbd1062c39adefe +file TCL01-BRMCT BRMCT_recal_reads.bai Index File tumor cell line sample, TCL01-BRMCT: bam index of WES reads 5993984 75a569264267e649c6f673593d227f2e +file TCL01-BRMCT BRMCT_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-BRMCT: WES reads to CanFam3.1 12734958795 7dd610733ab4a545ed180b839557d742 +file TCL01-C2 C2_recal_reads.bai Index File tumor cell line sample, TCL01-C2: bam index of WES reads 5952792 bcb37314c12165b79fff0af32b954e2d +file TCL01-C2 C2_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-C2: WES reads to CanFam3.1 14206860537 2732ae20e0d04330ff8d6dcae56fc541 +file TCL01-Cindy CINDY_recal_reads.bai Index File tumor cell line sample, TCL01-Cindy: bam index of WES reads 6045320 70f7cb898b5bc9dae2a6e0f776d2f25e +file TCL01-Cindy CINDY_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-Cindy: WES reads to CanFam3.1 11321375167 b5315f52dd138f64408d0b2717827be7 +file TCL01-CLBL1 CLBL1_recal_reads.bai Index File tumor cell line sample, TCL01-CLBL1: bam index of WES reads 6089344 91f881d13abc07ecb2a9acda49ec6592 +file TCL01-CLBL1 CLBL1_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-CLBL1: WES reads to CanFam3.1 12879642030 2b703e160fd67bd600bc06c4e5194dbc +file TCL01-CLL-1390 CLL1390_recal_reads.bai Index File tumor cell line sample, TCL01-CLL-1390: bam index of WES reads 5940688 6f981ad147ca14172d90bb71ee2d6b47 +file TCL01-CLL-1390 CLL1390_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-CLL-1390: WES reads to CanFam3.1 11063183792 6e5f2d1b70e1a15aa8161d8ff08b4f3c +file TCL01-CML-6M CML6M_recal_reads.bai Index File tumor cell line sample, TCL01-CML-6M: bam index of WES reads 6017352 fd4f31e0639812fc9720eec8c1eaab5e +file TCL01-CML-6M CML6M_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-CML-6M: WES reads to CanFam3.1 13819912565 ff81883bb52db4529684baf9d08f0d47 +file TCL01-CML-10C2 CML8410C2_recal_reads.bai Index File tumor cell line sample, TCL01-CML-10C2: bam index of WES reads 5775352 c768ea54e7d2582abfc0e879a56e64bd +file TCL01-CML-10C2 CML8410C2_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-CML-10C2: WES reads to CanFam3.1 11547785491 341d0de70c749743ba302224523bb282 +file TCL01-CMT12 CMT12_recal_reads.bai Index File tumor cell line sample, TCL01-CMT12: bam index of WES reads 5861768 f3c6e5275164b4bd169d48ca3eccc8c9 +file TCL01-CMT12 CMT12_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-CMT12: WES reads to CanFam3.1 11503041279 3674662154f40c618800e00fe1a01cff +file TCL01-CTAC CTAC_recal_reads.bai Index File tumor cell line sample, TCL01-CTAC: bam index of WES reads 5967232 000acc71589ef0f0651b6568f74db029 +file TCL01-CTAC CTAC_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-CTAC: WES reads to CanFam3.1 12333386882 f820e4a1903de38de47032daabd368be +file TCL01-D-17 D17_recal_reads.bai Index File tumor cell line sample, TCL01-D-17: bam index of WES reads 6167080 65b6e7f9863ac7702245aec0ace69bec +file TCL01-D-17 D17_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-D-17: WES reads to CanFam3.1 14885423514 743f1238a56a582ea3b368ab28e1429f +file TCL01-DEN-HSA DENNY_recal_reads.bai Index File tumor cell line sample, TCL01-DEN-HSA: bam index of WES reads 6009952 580df4374c123151ce6c6b9c9502ca5a +file TCL01-DEN-HSA DENNY_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-DEN-HSA: WES reads to CanFam3.1 11416481531 62e9ca8c6c9a8dbf56a06fb63e433be4 +file TCL01-DH82 DH82_recal_reads.bai Index File tumor cell line sample, TCL01-DH82: bam index of WES reads 6038128 89a41178d5b5f36a6c4a25c3d4b67348 +file TCL01-DH82 DH82_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-DH82: WES reads to CanFam3.1 15276960482 7a4be07d1e8558140d0fd98eff7b9a0f +file TCL01-Gracie GRACIE_recal_reads.bai Index File tumor cell line sample, TCL01-Gracie: bam index of WES reads 6272816 9ab3f467c8ff7be49da8110672e93b1a +file TCL01-Gracie GRACIE_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-Gracie: WES reads to CanFam3.1 20107363220 c1d290ecf6391f5eff97b0fb509e2fe7 +file TCL01-HMPOS HMPOS_recal_reads.bai Index File tumor cell line sample, TCL01-HMPOS: bam index of WES reads 5922504 9dd5edeef4f8ea4b31e3e467e309f58b +file TCL01-HMPOS HMPOS_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-HMPOS: WES reads to CanFam3.1 13004970608 fde03039d6d2e640928f5393c12a5ed6 +file TCL01-Jones JONES_recal_reads.bai Index File tumor cell line sample, TCL01-Jones: bam index of WES reads 6019640 4ca1cf7a0ec588a521bd2639a42030c7 +file TCL01-Jones JONES_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-Jones: WES reads to CanFam3.1 15484551373 b209406b089ff9e6c214815028205e03 +file TCL01-Kinsey KINSEY_recal_reads.bai Index File tumor cell line sample, TCL01-Kinsey: bam index of WES reads 6002392 c9a9d5a198b71b82ece903a071e412c3 +file TCL01-Kinsey KINSEY_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-Kinsey: WES reads to CanFam3.1 13028953715 64fb3640a3d8c83ef9c55c6d988a9f0b +file TCL01-McKinley MACKINLEY_recal_reads.bai Index File tumor cell line sample, TCL01-McKinley: bam index of WES reads 5991712 5da19e58266a35086cf252f4744f93e6 +file TCL01-McKinley MACKINLEY_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-McKinley: WES reads to CanFam3.1 15930203963 df11b00c83de825d262417103d364e1a +file TCL01-Moresco MORESCO_recal_reads.bai Index File tumor cell line sample, TCL01-Moresco: bam index of WES reads 5980688 f93ca8cd177eabad0e7f9c79c035f9e9 +file TCL01-Moresco MORESCO_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-Moresco: WES reads to CanFam3.1 12969130310 f5d91b56967b5375331410912c54dcc8 +file TCL01-Nike NIKE_recal_reads.bai Index File tumor cell line sample, TCL01-Nike: bam index of WES reads 5982416 3b6917d9ea7ae9e4f35980bf3b60a88e +file TCL01-Nike NIKE_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-Nike: WES reads to CanFam3.1 13834591537 757ff28e42b24d2261179bccbf696f14 +file TCL01-OS2.4 OS2-4_recal_reads.bai Index File tumor cell line sample, TCL01-OS2.4: bam index of WES reads 6132328 7d3b98a5789bf9270e3292fae787f60b +file TCL01-OS2.4 OS2-4_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-OS2.4: WES reads to CanFam3.1 16406343532 d31aeeb6f44600c36cc3838bfc4c8af6 +file TCL01-OSA8 OSA8_recal_reads.bai Index File tumor cell line sample, TCL01-OSA8: bam index of WES reads 6169168 6de0d625b4c9995c39c0e6fcd3c79e9b +file TCL01-OSA8 OSA8_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-OSA8: WES reads to CanFam3.1 15295197872 b3dbc062e48c7db29596e25f90b3bc7a +file TCL01-OSW OSW_recal_reads.bai Index File tumor cell line sample, TCL01-OSW: bam index of WES reads 6129712 fe2a0df060c8d40be92ef0e835255df4 +file TCL01-OSW OSW_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-OSW: WES reads to CanFam3.1 15645298941 b7a0879015e0b583e4a20a54ab08abeb +file TCL01-Parks PARKS_recal_reads.bai Index File tumor cell line sample, TCL01-Parks: bam index of WES reads 6534840 2b466cafddc7b428ff05da1a15dc6cf6 +file TCL01-Parks PARKS_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-Parks: WES reads to CanFam3.1 20117760429 34d6fdeef92bbf19b6887f0b7752116a +file TCL01-SB SB_recal_reads.bai Index File tumor cell line sample, TCL01-SB: bam index of WES reads 6173640 8f4fc8218a773798b81d1573b811c8da +file TCL01-SB SB_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-SB: WES reads to CanFam3.1 15742684377 f8f253afb557f0e33a0a864a4d862e7b +file TCL01-STSA-1 STS-1_recal_reads.bai Index File tumor cell line sample, TCL01-STSA-1: bam index of WES reads 6178592 09abe8721e1603d86e8286eff9d24d87 +file TCL01-STSA-1 STS-1_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-STSA-1: WES reads to CanFam3.1 16771819055 c4ce1f8bcc879a4838a81ea5e8843be9 +file TCL01-Tyler1 TYLER1_recal_reads.bai Index File tumor cell line sample, TCL01-Tyler1: bam index of WES reads 5936288 3ab276af9b2f8dcf8abba7af49c954a6 +file TCL01-Tyler1 TYLER1_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-Tyler1: WES reads to CanFam3.1 11471388290 2f3a05cd811bfeb115f3b897cec6a12b +file TCL01-Tyler2 TYLER2_recal_reads.bai Index File tumor cell line sample, TCL01-Tyler2: bam index of WES reads 6128568 fc354a42685615be86e35d4d1018239e +file TCL01-Tyler2 TYLER2_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-Tyler2: WES reads to CanFam3.1 15424341682 fd54a81f8508833a966b241293793218 +file TCL01-Vogel VOGEL_recal_reads.bai Index File tumor cell line sample, TCL01-Vogel: bam index of WES reads 6059208 9b5111bd59cadff5c0cc00c3182b5334 +file TCL01-Vogel VOGEL_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-Vogel: WES reads to CanFam3.1 22941297095 5a33ed689898579edde9ab4bf7ac6d17 +file TCL01-N-1146 N-1146_recal_reads.bai Index File normal sample, TCL01-N-1146: bam index of WES reads 5966640 871146c4742be026a8845a1eacf7120d +file TCL01-N-1146 N-1146_recal_reads.bam Whole Exome Sequence File normal sample, TCL01-N-1146: WES reads to CanFam3.1 13709569910 c6f0a5dcfaf8b52b0b9c30df72511c26 +file TCL01-N-1344 N-1344_recal_reads.bai Index File normal sample, TCL01-N-1344: bam index of WES reads 5483208 3bb1c7b36476ea8825a67506e3dbbe2d +file TCL01-N-1344 N-1344_recal_reads.bam Whole Exome Sequence File normal sample, TCL01-N-1344: WES reads to CanFam3.1 8496493381 52c6830d322d10c226e62a03be03aca4 +file TCL01-N-166408 N-166408_recal_reads.bai Index File normal sample, TCL01-N-166408: bam index of WES reads 5435520 43d7c317a765880bfc6c187dde17f620 +file TCL01-N-166408 N-166408_recal_reads.bam Whole Exome Sequence File normal sample, TCL01-N-166408: WES reads to CanFam3.1 9536035091 e08b87efd448b31115f0b854d2778cfd +file TCL01-N-172160 N-172160_recal_reads.bai Index File normal sample, TCL01-N-172160: bam index of WES reads 5588544 ed073737170ed2a5972e979074f6d80f +file TCL01-N-172160 N-172160_recal_reads.bam Whole Exome Sequence File normal sample, TCL01-N-172160: WES reads to CanFam3.1 8806593257 1ab700451aa54c8f36495fc852c50807 +file TCL01-N-1776 N-1776_recal_reads.bai Index File normal sample, TCL01-N-1776: bam index of WES reads 5632672 f7e0e0e15ed30c96abe9a7ca932d48a8 +file TCL01-N-1776 N-1776_recal_reads.bam Whole Exome Sequence File normal sample, TCL01-N-1776: WES reads to CanFam3.1 9211871132 93f70d106718812541d0cc9b9b2a3f5e +file TCL01-N-1866 N-1866_recal_reads.bai Index File normal sample, TCL01-N-1866: bam index of WES reads 5817080 f6206908d6f88ad46ad0dd29a7520da4 +file TCL01-N-1866 N-1866_recal_reads.bam Whole Exome Sequence File normal sample, TCL01-N-1866: WES reads to CanFam3.1 11810859656 5a9937c8d6143eca6bd77de6699a7817 +file TCL01-N-353 N-353_recal_reads.bai Index File normal sample, TCL01-N-353: bam index of WES reads 5572704 bfc15de56f00eb38c7fa96a43ea6d57f +file TCL01-N-353 N-353_recal_reads.bam Whole Exome Sequence File normal sample, TCL01-N-353: WES reads to CanFam3.1 8616102202 3c7e5c329e781b192e0b804ba5fc94f6 +file TCL01-N-Bella N-Bella_recal_reads.bai Index File normal sample, TCL01-N-Bella: bam index of WES reads 5677384 29e49563d47e23d946a1bb0516c489cc +file TCL01-N-Bella N-Bella_recal_reads.bam Whole Exome Sequence File normal sample, TCL01-N-Bella: WES reads to CanFam3.1 12052962019 34b250eed7221d0b53b6f425208f3651 +file TCL01-N-CSU7 N-csu7_recal_reads.bai Index File normal sample, TCL01-N-CSU7: bam index of WES reads 5658952 bb0d4e4867d234bf5ef04c59d97726ad +file TCL01-N-CSU7 N-csu7_recal_reads.bam Whole Exome Sequence File normal sample, TCL01-N-CSU7: WES reads to CanFam3.1 13349785456 ecf5dd62861abf5f12b678ef4a9a7211 +file TCL01-N-CSU9 N-CSU9_recal_reads.bai Index File normal sample, TCL01-N-CSU9: bam index of WES reads 5544840 a62599e81a72d19b6d4640b6516bcae5 +file TCL01-N-CSU9 N-CSU9_recal_reads.bam Whole Exome Sequence File normal sample, TCL01-N-CSU9: WES reads to CanFam3.1 12055125754 0337180cffbc95e501f4c49289068d73 +file TCL01-N-VRCC3 N-vrcc3_recal_reads.bai Index File normal sample, TCL01-N-VRCC3: bam index of WES reads 5605400 2164cc3caf1d69ba3a5acaae222b13e1 +file TCL01-N-VRCC3 N-vrcc3_recal_reads.bam Whole Exome Sequence File normal sample, TCL01-N-VRCC3: WES reads to CanFam3.1 12165094093 8ea6e5e94b251c1bbc3c121f26646095 +file TCL01-N-VRCC7 N-VRCC7_recal_reads.bai Index File normal sample, TCL01-N-VRCC7: bam index of WES reads 5559040 505553c39256f2db02776a8d332ffdfc +file TCL01-N-VRCC7 N-VRCC7_recal_reads.bam Whole Exome Sequence File normal sample, TCL01-N-VRCC7: WES reads to CanFam3.1 11179218619 921b99b5ba416713c76c4be9e32f1399 +file TCL01-N-Zada N-Zada_recal_reads.bai Index File normal sample, TCL01-N-Zada: bam index of WES reads 5518024 b3e1f7a993369723c4e5763131425b84 +file TCL01-N-Zada N-Zada_recal_reads.bam Whole Exome Sequence File normal sample, TCL01-N-Zada: WES reads to CanFam3.1 11175904110 c92d6de4ae3bc347604fc6a3eb29ee05 diff --git a/model-desc/TCL01 Loading File Example Set/TCL01-File_Transfer_Manifest - Study Files.tsv b/model-desc/TCL01 Loading File Example Set/TCL01-File_Transfer_Manifest - Study Files.tsv new file mode 100644 index 0000000..f862295 --- /dev/null +++ b/model-desc/TCL01 Loading File Example Set/TCL01-File_Transfer_Manifest - Study Files.tsv @@ -0,0 +1,4 @@ +"type" " case.case_id" " study.clinical_study_designation" " sample.sample_id" " diagnosis.diagnosis_id" "file_name" "file_type" "file_description" "original_file_size" "original_md5sum" +"file" "TCL01" "TCL01_CellLine_CDS_Variants.csv" "Supplemental Data File" "Cell line coding region somatic variants " 4173475 "b6cb025a2062a8f88f17e6314e6be44c" +"file" "TCL01" "TCL01_CellLineSourcing_STRs_DrugSensitivity.xlsx" "Supplemental Data File" "Cell line sourcing data, STR analysis, and drug sensitivity assay" 41862 "fc07413be62d11ff99ad33899b6fbfe7" +"file" "TCL01" "TCL01_Study_Protocol.docx" "Study Protocol" "Background, methods, and key results" 219492 "148ab1ba4faf414842cbf64750cd3a7a" diff --git a/model-desc/TCL01 Loading File Example Set/TCL01-case.txt b/model-desc/TCL01 Loading File Example Set/TCL01-case.txt new file mode 100644 index 0000000..7480c05 --- /dev/null +++ b/model-desc/TCL01 Loading File Example Set/TCL01-case.txt @@ -0,0 +1,46 @@ +type study.clinical_study_designation case_id patient_id patient_first_name +case TCL01 TCL01-Angus Angus Angus +case TCL01 TCL01-Bliley Bliley Socks +case TCL01 TCL01-Kinsey Kinsey Kinsey +case TCL01 TCL01-Tyler Tyler Tyler +case TCL01 TCL01-Cindy Cindy Cindy +case TCL01 TCL01-DEN-HSA DEN-HSA +case TCL01 TCL01-SB SB +case TCL01 TCL01-DH82 DH82 +case TCL01 TCL01-Nike Nike Nike +case TCL01 TCL01-CLL-1390 CLL-1390 +case TCL01 TCL01-17-71 17-71 +case TCL01 TCL01-CLBL1 CLBL1 +case TCL01 TCL01-OSW OSW +case TCL01 TCL01-CMT12 CMT12 +case TCL01 TCL01-BRMCT BRMCT +case TCL01 TCL01-C2 C2 +case TCL01 TCL01-17CM98 17CM98 +case TCL01 TCL01-CML-10C2 CML-10C2 +case TCL01 TCL01-CML-6M CML-6M +case TCL01 TCL01-Jones Jones +case TCL01 TCL01-Parks Parks +case TCL01 TCL01-Abrams Abrams +case TCL01 TCL01-D-17 D-17 +case TCL01 TCL01-Gracie Gracie Gracie +case TCL01 TCL01-HMPOS HMPOS +case TCL01 TCL01-McKinley McKinley +case TCL01 TCL01-Moresco Moresco +case TCL01 TCL01-OS2.4 OS2.4 +case TCL01 TCL01-OSA8 OSA8 +case TCL01 TCL01-Vogel Vogel +case TCL01 TCL01-STSA-1 STSA-1 +case TCL01 TCL01-CTAC CTAC +case TCL01 TCL01-N-1344 N-1344 +case TCL01 TCL01-N-1866 N-1866 +case TCL01 TCL01-N-1146 N-1146 +case TCL01 TCL01-N-1776 N-1776 +case TCL01 TCL01-N-353 N-353 +case TCL01 TCL01-N-166408 N-166408 +case TCL01 TCL01-N-172160 N-172160 +case TCL01 TCL01-N-Bella N-Bella Bella +case TCL01 TCL01-N-Zada N-Zada Zada +case TCL01 TCL01-N-CSU7 N-CSU7 +case TCL01 TCL01-N-CSU9 N-CSU9 +case TCL01 TCL01-N-VRCC3 N-VRCC3 +case TCL01 TCL01-N-VRCC7 N-VRCC7 diff --git a/model-desc/TCL01 Loading File Example Set/TCL01-demographic.txt b/model-desc/TCL01 Loading File Example Set/TCL01-demographic.txt new file mode 100644 index 0000000..f5ae627 --- /dev/null +++ b/model-desc/TCL01 Loading File Example Set/TCL01-demographic.txt @@ -0,0 +1,46 @@ +type case.case_id demographic_id breed patient_age_at_enrollment sex neutered_indicator weight +demographic TCL01-Angus TCL01-Angus Scottish Terrier Male Unknown +demographic TCL01-Bliley TCL01-Bliley Basenji 10 Female Yes 17 +demographic TCL01-Kinsey TCL01-Kinsey Australian Shepherd Unknown Unknown +demographic TCL01-Tyler TCL01-Tyler Beagle 8 Male Yes +demographic TCL01-Cindy TCL01-Cindy Labrador Retriever 3 Female Unknown +demographic TCL01-DEN-HSA TCL01-DEN-HSA Golden Retriever 11 Male Yes +demographic TCL01-SB TCL01-SB German Shepherd Dog 9 Male Unknown +demographic TCL01-DH82 TCL01-DH82 Golden Retriever 10 Male No +demographic TCL01-Nike TCL01-Nike Unknown Unknown Unknown +demographic TCL01-CLL-1390 TCL01-CLL-1390 Unknown Unknown Unknown +demographic TCL01-17-71 TCL01-17-71 Unknown Unknown Unknown +demographic TCL01-CLBL1 TCL01-CLBL1 Bernese Mountain Dog 8 Male Unknown +demographic TCL01-OSW TCL01-OSW Airedale Terrier 5.5 Male Unknown +demographic TCL01-CMT12 TCL01-CMT12 Poodle Female Unknown +demographic TCL01-BRMCT TCL01-BRMCT Unknown Unknown Unknown +demographic TCL01-C2 TCL01-C2 Unknown Female Unknown +demographic TCL01-17CM98 TCL01-17CM98 Unknown Unknown Unknown +demographic TCL01-CML-10C2 TCL01-CML-10C2 Unknown Unknown Unknown +demographic TCL01-CML-6M TCL01-CML-6M Mixed Breed 8 Unknown Unknown +demographic TCL01-Jones TCL01-Jones Miniature Dachshund 14 Female Yes 6.2 +demographic TCL01-Parks TCL01-Parks Labrador Retriever 12 Female Yes 32 +demographic TCL01-Abrams TCL01-Abrams Rottweiler 2.5 Male Unknown 40.8 +demographic TCL01-D-17 TCL01-D-17 Poodle 11 Female Unknown +demographic TCL01-Gracie TCL01-Gracie Unknown Unknown Unknown +demographic TCL01-HMPOS TCL01-HMPOS Mixed Breed 1.5 Male Unknown +demographic TCL01-McKinley TCL01-McKinley Unknown Unknown Unknown +demographic TCL01-Moresco TCL01-Moresco Unknown Unknown Unknown +demographic TCL01-OS2.4 TCL01-OS2.4 Golden Retriever 5 Unknown Unknown +demographic TCL01-OSA8 TCL01-OSA8 Rottweiler 2 Male Unknown +demographic TCL01-Vogel TCL01-Vogel Unknown Unknown Unknown +demographic TCL01-STSA-1 TCL01-STSA-1 Golden Retriever 7 Male Yes +demographic TCL01-CTAC TCL01-CTAC Boxer 7 Female Unknown +demographic TCL01-N-1344 TCL01-N-1344 Labrador Retriever Male Yes 42.8 +demographic TCL01-N-1866 TCL01-N-1866 Greyhound Female Yes 23.4 +demographic TCL01-N-1146 TCL01-N-1146 Bernese Mountain Dog Male Yes 47.2 +demographic TCL01-N-1776 TCL01-N-1776 Rottweiler Female Yes 36 +demographic TCL01-N-353 TCL01-N-353 Mixed Breed Male Yes 23.6 +demographic TCL01-N-166408 TCL01-N-166408 Mixed Breed Male Yes 47 +demographic TCL01-N-172160 TCL01-N-172160 Shetland Sheepdog Female Yes 16 +demographic TCL01-N-Bella TCL01-N-Bella Golden Retriever Female Yes 34 +demographic TCL01-N-Zada TCL01-N-Zada Rhodesian Ridgeback Female Yes 38.8 +demographic TCL01-N-CSU7 TCL01-N-CSU7 Golden Retriever Male Yes 27.4 +demographic TCL01-N-CSU9 TCL01-N-CSU9 Cocker Spaniel Female Yes 13.3 +demographic TCL01-N-VRCC3 TCL01-N-VRCC3 Golden Retriever Female Yes +demographic TCL01-N-VRCC7 TCL01-N-VRCC7 Boxer Female Yes diff --git a/model-desc/TCL01 Loading File Example Set/TCL01-diagnosis.txt b/model-desc/TCL01 Loading File Example Set/TCL01-diagnosis.txt new file mode 100644 index 0000000..0bc216f --- /dev/null +++ b/model-desc/TCL01 Loading File Example Set/TCL01-diagnosis.txt @@ -0,0 +1,46 @@ +type case.case_id diagnosis_id disease_term primary_disease_site stage_of_disease best_response treatment_data follow_up_data pathology_report concurrent_disease concurrent_disease_type +diagnosis TCL01-Angus TCL01-Angus Bladder Cancer Unknown Unknown Not Applicable Yes No No Unknown +diagnosis TCL01-Bliley TCL01-Bliley Bladder Cancer Distal Urethra Unknown Not Applicable Yes No No No +diagnosis TCL01-Kinsey TCL01-Kinsey Bladder Cancer Unknown Unknown Not Applicable Yes No No Unknown +diagnosis TCL01-Tyler TCL01-Tyler Bladder Cancer Urethra, Prostate Unknown Not Applicable Yes No No Unknown +diagnosis TCL01-Cindy TCL01-Cindy Hemangiosarcoma Unknown Unknown Not Applicable Yes No No Unknown +diagnosis TCL01-DEN-HSA TCL01-DEN-HSA Hemangiosarcoma Kidney Unknown Not Applicable Yes No No Unknown +diagnosis TCL01-SB TCL01-SB Hemangiosarcoma Subcutis Unknown Not Applicable Yes No No Unknown +diagnosis TCL01-DH82 TCL01-DH82 Histiocytic Sarcoma Bone Marrow Unknown Not Applicable Yes No No Unknown +diagnosis TCL01-Nike TCL01-Nike Histiocytic Sarcoma Unknown Unknown Not Applicable Yes No No Unknown +diagnosis TCL01-CLL-1390 TCL01-CLL-1390 T Cell Leukemia Unknown Unknown Not Applicable Yes No No Unknown +diagnosis TCL01-17-71 TCL01-17-71 B Cell Lymphoma Lymph Node Unknown Not Applicable Yes No No Unknown +diagnosis TCL01-CLBL1 TCL01-CLBL1 B Cell Lymphoma Lymph Node Unknown Not Applicable Yes No No Unknown +diagnosis TCL01-OSW TCL01-OSW Lymphoma Pleural Cavity Unknown Not Applicable Yes No No Unknown +diagnosis TCL01-CMT12 TCL01-CMT12 Mammary Cancer Mammary Gland Unknown Not Applicable Yes No No Unknown +diagnosis TCL01-BRMCT TCL01-BRMCT Mast Cell Tumor Subcutis Unknown Not Applicable Yes No No Unknown +diagnosis TCL01-C2 TCL01-C2 Mast Cell Tumor Subcutis Unknown Not Applicable Yes No No Unknown +diagnosis TCL01-17CM98 TCL01-17CM98 Melanoma Mouth Unknown Not Applicable Yes No No Unknown +diagnosis TCL01-CML-10C2 TCL01-CML-10C2 Melanoma Skin Unknown Not Applicable Yes No No Unknown +diagnosis TCL01-CML-6M TCL01-CML-6M Melanoma Skin Unknown Not Applicable Yes No No Unknown +diagnosis TCL01-Jones TCL01-Jones Melanoma Mouth Unknown Not Applicable Yes No No Unknown +diagnosis TCL01-Parks TCL01-Parks Melanoma Mouth Unknown Not Applicable Yes No No Unknown +diagnosis TCL01-Abrams TCL01-Abrams Osteosarcoma Bone (Appendicular) Unknown Not Applicable Yes No No Unknown +diagnosis TCL01-D-17 TCL01-D-17 Osteosarcoma Bone (Appendicular) Unknown Not Applicable Yes No No Unknown +diagnosis TCL01-Gracie TCL01-Gracie Osteosarcoma Bone (Appendicular) Unknown Not Applicable Yes No No Unknown +diagnosis TCL01-HMPOS TCL01-HMPOS Osteosarcoma Bone (Appendicular) Unknown Not Applicable Yes No No Unknown +diagnosis TCL01-McKinley TCL01-McKinley Osteosarcoma Bone (Appendicular) Unknown Not Applicable Yes No No Unknown +diagnosis TCL01-Moresco TCL01-Moresco Osteosarcoma Bone (Appendicular) Unknown Not Applicable Yes No No Unknown +diagnosis TCL01-OS2.4 TCL01-OS2.4 Osteosarcoma Bone (Appendicular) Unknown Not Applicable Yes No No Unknown +diagnosis TCL01-OSA8 TCL01-OSA8 Osteosarcoma Bone (Appendicular) Unknown Not Applicable Yes No No Unknown +diagnosis TCL01-Vogel TCL01-Vogel Osteosarcoma Bone (Appendicular) Unknown Not Applicable Yes No No Unknown +diagnosis TCL01-STSA-1 TCL01-STSA-1 Soft Tissue Sarcoma Carpus Unknown Not Applicable Yes No No Unknown +diagnosis TCL01-CTAC TCL01-CTAC Thyroid Cancer Thyroid Gland Unknown Not Applicable Yes No No Unknown +diagnosis TCL01-N-1344 TCL01-N-1344 Splenic Hyperplasia Spleen Not Applicable Not Applicable No No No Unknown +diagnosis TCL01-N-1866 TCL01-N-1866 Splenic Hematoma Spleen Not Applicable Not Applicable No No No Unknown +diagnosis TCL01-N-1146 TCL01-N-1146 Lipoma Chest Wall Not Applicable Not Applicable No No No Unknown +diagnosis TCL01-N-1776 TCL01-N-1776 Fibrolipoma Shoulder Not Applicable Not Applicable No No No Unknown +diagnosis TCL01-N-353 TCL01-N-353 Bladder Cancer Bladder Unknown Not Applicable No No No Unknown +diagnosis TCL01-N-166408 TCL01-N-166408 Bladder Cancer Bladder Unknown Not Applicable No No No Unknown +diagnosis TCL01-N-172160 TCL01-N-172160 Bladder Cancer Bladder Unknown Not Applicable No No No Unknown +diagnosis TCL01-N-Bella TCL01-N-Bella B Cell Lymphoma Lymph Node Unknown Not Applicable No No No Unknown +diagnosis TCL01-N-Zada TCL01-N-Zada B Cell Lymphoma Lymph Node Unknown Not Applicable No No No Unknown +diagnosis TCL01-N-CSU7 TCL01-N-CSU7 B Cell Lymphoma Lymph Node Unknown Not Applicable No No No Unknown +diagnosis TCL01-N-CSU9 TCL01-N-CSU9 B Cell Lymphoma Lymph Node Unknown Not Applicable No No No Unknown +diagnosis TCL01-N-VRCC3 TCL01-N-VRCC3 B Cell Lymphoma Lymph Node Unknown Not Applicable No No No Unknown +diagnosis TCL01-N-VRCC7 TCL01-N-VRCC7 B Cell Lymphoma Lymph Node Unknown Not Applicable No No No Unknown diff --git a/model-desc/TCL01 Loading File Example Set/TCL01-enrollment.txt b/model-desc/TCL01 Loading File Example Set/TCL01-enrollment.txt new file mode 100644 index 0000000..58e7b86 --- /dev/null +++ b/model-desc/TCL01 Loading File Example Set/TCL01-enrollment.txt @@ -0,0 +1,46 @@ +type case.case_id enrollment_id site_short_name +enrollment TCL01-Angus TCL01-Angus Tufts +enrollment TCL01-Bliley TCL01-Bliley CSU +enrollment TCL01-Kinsey TCL01-Kinsey Tufts +enrollment TCL01-Tyler TCL01-Tyler Tufts +enrollment TCL01-Cindy TCL01-Cindy UI +enrollment TCL01-DEN-HSA TCL01-DEN-HSA UWM +enrollment TCL01-SB TCL01-SB UWM +enrollment TCL01-DH82 TCL01-DH82 ATCC +enrollment TCL01-Nike TCL01-Nike MSU +enrollment TCL01-CLL-1390 TCL01-CLL-1390 UCD +enrollment TCL01-17-71 TCL01-17-71 UPENN +enrollment TCL01-CLBL1 TCL01-CLBL1 Aus +enrollment TCL01-OSW TCL01-OSW OSU +enrollment TCL01-CMT12 TCL01-CMT12 AU +enrollment TCL01-BRMCT TCL01-BRMCT UCSF +enrollment TCL01-C2 TCL01-C2 UCSF +enrollment TCL01-17CM98 TCL01-17CM98 UWM +enrollment TCL01-CML-10C2 TCL01-CML-10C2 AU +enrollment TCL01-CML-6M TCL01-CML-6M AU +enrollment TCL01-Jones TCL01-Jones CSU +enrollment TCL01-Parks TCL01-Parks CSU +enrollment TCL01-Abrams TCL01-Abrams CSU/UWM +enrollment TCL01-D-17 TCL01-D-17 ATCC +enrollment TCL01-Gracie TCL01-Gracie UWM +enrollment TCL01-HMPOS TCL01-HMPOS Tokyo +enrollment TCL01-McKinley TCL01-McKinley CSU +enrollment TCL01-Moresco TCL01-Moresco UWM +enrollment TCL01-OS2.4 TCL01-OS2.4 WSU +enrollment TCL01-OSA8 TCL01-OSA8 UM +enrollment TCL01-Vogel TCL01-Vogel CSU +enrollment TCL01-STSA-1 TCL01-STSA-1 UI +enrollment TCL01-CTAC TCL01-CTAC OSU +enrollment TCL01-N-1344 TCL01-N-1344 CSU +enrollment TCL01-N-1866 TCL01-N-1866 CSU +enrollment TCL01-N-1146 TCL01-N-1146 CSU +enrollment TCL01-N-1776 TCL01-N-1776 CSU +enrollment TCL01-N-353 TCL01-N-353 CSU +enrollment TCL01-N-166408 TCL01-N-166408 CSU +enrollment TCL01-N-172160 TCL01-N-172160 CSU +enrollment TCL01-N-Bella TCL01-N-Bella CSU +enrollment TCL01-N-Zada TCL01-N-Zada CSU +enrollment TCL01-N-CSU7 TCL01-N-CSU7 CSU +enrollment TCL01-N-CSU9 TCL01-N-CSU9 CSU +enrollment TCL01-N-VRCC3 TCL01-N-VRCC3 CSU +enrollment TCL01-N-VRCC7 TCL01-N-VRCC7 CSU diff --git a/model-desc/TCL01 Loading File Example Set/TCL01-principal_investigator.txt b/model-desc/TCL01 Loading File Example Set/TCL01-principal_investigator.txt new file mode 100644 index 0000000..1d96ffc --- /dev/null +++ b/model-desc/TCL01 Loading File Example Set/TCL01-principal_investigator.txt @@ -0,0 +1,2 @@ +type study.clinical_study_designation pi_first_name pi_last_name pi_middle_initial +principal_investigator TCL01 Dawn Duval L \ No newline at end of file diff --git a/model-desc/TCL01 Loading File Example Set/TCL01-publication.txt b/model-desc/TCL01 Loading File Example Set/TCL01-publication.txt new file mode 100644 index 0000000..aeea34e --- /dev/null +++ b/model-desc/TCL01 Loading File Example Set/TCL01-publication.txt @@ -0,0 +1,2 @@ +type study.clinical_study_designation publication_title authorship year_of_publication journal_citation digital_object_id pubmed_id +publication TCL01 Identifying Candidate Druggable Targets in Canine Cancer Cell Lines Using Whole-Exome Sequencing Das S et al 2019 Mol Cancer Ther 18 (8): 1460-1471. 10.1158/1535-7163.MCT-18-1346 31175136 \ No newline at end of file diff --git a/model-desc/TCL01 Loading File Example Set/TCL01-sample.txt b/model-desc/TCL01 Loading File Example Set/TCL01-sample.txt new file mode 100644 index 0000000..d6128d6 --- /dev/null +++ b/model-desc/TCL01 Loading File Example Set/TCL01-sample.txt @@ -0,0 +1,47 @@ +type case.case_id sample_id physical_sample_type general_sample_pathology tumor_sample_origin summarized_sample_type sample_site sample_chronology specific_sample_pathology tumor_grade date_of_sample_collection sample_preservation necropsy_sample percentage_tumor +sample TCL01-Angus TCL01-Angus Cell Line Malignant Primary Tumor Cell Line Bladder Not Applicable Urothelial Carcinoma Unknown Not Applicable No 100% +sample TCL01-Bliley TCL01-Bliley Cell Line Malignant Primary Tumor Cell Line Distal Urethra Not Applicable Urothelial Carcinoma Unknown Not Applicable No 100% +sample TCL01-Kinsey TCL01-Kinsey Cell Line Malignant Primary Tumor Cell Line Bladder Not Applicable Urothelial Carcinoma Unknown Not Applicable No 100% +sample TCL01-Tyler TCL01-Tyler1 Cell Line Malignant Primary Tumor Cell Line Bladder Not Applicable Urothelial Carcinoma Unknown Not Applicable No 100% +sample TCL01-Tyler TCL01-Tyler2 Cell Line Malignant Primary Tumor Cell Line Bladder Not Applicable Urothelial Carcinoma Unknown Not Applicable No 100% +sample TCL01-Cindy TCL01-Cindy Cell Line Malignant Primary Tumor Cell Line Spleen Not Applicable Hemangiosarcoma Unknown Not Applicable No 100% +sample TCL01-DEN-HSA TCL01-DEN-HSA Cell Line Malignant Primary Tumor Cell Line Kidney Not Applicable Hemangiosarcoma Unknown Not Applicable No 100% +sample TCL01-SB TCL01-SB Cell Line Malignant Primary Tumor Cell Line Skin Not Applicable Hemangiosarcoma Unknown Not Applicable No 100% +sample TCL01-DH82 TCL01-DH82 Cell Line Malignant Primary Tumor Cell Line Bone Marrow Not Applicable Histiocytic Sarcoma Unknown Not Applicable Yes 100% +sample TCL01-Nike TCL01-Nike Cell Line Malignant Primary Tumor Cell Line Unknown Not Applicable Histiocytic Sarcoma Unknown Not Applicable No 100% +sample TCL01-CLL-1390 TCL01-CLL-1390 Cell Line Malignant Primary Tumor Cell Line Unknown Not Applicable Primitive T-Cell Leukemia Unknown Not Applicable No 100% +sample TCL01-17-71 TCL01-17-71 Cell Line Malignant Primary Tumor Cell Line Lymph Node Not Applicable B Cell Lymphoma Unknown Not Applicable No 100% +sample TCL01-CLBL1 TCL01-CLBL1 Cell Line Malignant Primary Tumor Cell Line Lymph Node, Popliteal Not Applicable B Cell Lymphoma Unknown Not Applicable No 100% +sample TCL01-OSW TCL01-OSW Cell Line Malignant Metastatic Tumor Cell Line (metastasis-derived) Pleural Effusion Not Applicable T Cell Lymphoma Unknown Not Applicable No 100% +sample TCL01-CMT12 TCL01-CMT12 Cell Line Malignant Primary Tumor Cell Line Mammary Gland Not Applicable Carcinoma Unknown Not Applicable No 100% +sample TCL01-BRMCT TCL01-BRMCT Cell Line Malignant Primary Tumor Cell Line Skin Not Applicable Mast Cell Tumor Unknown Not Applicable No 100% +sample TCL01-C2 TCL01-C2 Cell Line Malignant Primary Tumor Cell Line Skin Not Applicable Mast Cell Tumor Unknown Not Applicable No 100% +sample TCL01-17CM98 TCL01-17CM98 Cell Line Malignant Metastatic Tumor Cell Line (metastasis-derived) Lymph Node Not Applicable Melanoma Unknown Not Applicable No 100% +sample TCL01-CML-10C2 TCL01-CML-10C2 Cell Line Malignant Primary Tumor Cell Line Cutis Not Applicable Melanoma Unknown Not Applicable No 100% +sample TCL01-CML-6M TCL01-CML-6M Cell Line Malignant Metastatic Tumor Cell Line (metastasis-derived) Lymph Node Not Applicable Melanoma Unknown Not Applicable No 100% +sample TCL01-Jones TCL01-Jones Cell Line Malignant Unknown Tumor Cell Line Mouth Not Applicable Melanoma Unknown Not Applicable No 100% +sample TCL01-Parks TCL01-Parks Cell Line Malignant Unknown Tumor Cell Line Mouth Not Applicable Melanoma Unknown Not Applicable No 100% +sample TCL01-Abrams TCL01-Abrams Cell Line Malignant Metastatic Tumor Cell Line (metastasis-derived) Lung Not Applicable Osteosarcoma Unknown Not Applicable No 100% +sample TCL01-D-17 TCL01-D-17 Cell Line Malignant Metastatic Tumor Cell Line (metastasis-derived) Lung Not Applicable Osteosarcoma Unknown Not Applicable No 100% +sample TCL01-Gracie TCL01-Gracie Cell Line Malignant Primary Tumor Cell Line Bone Not Applicable Osteosarcoma Unknown Not Applicable No 100% +sample TCL01-HMPOS TCL01-HMPOS Cell Line Malignant Primary Tumor Cell Line Bone Not Applicable Osteosarcoma Unknown Not Applicable No 100% +sample TCL01-McKinley TCL01-McKinley Cell Line Malignant Primary Tumor Cell Line Bone Not Applicable Osteosarcoma Unknown Not Applicable No 100% +sample TCL01-Moresco TCL01-Moresco Cell Line Malignant Primary Tumor Cell Line Bone Not Applicable Osteosarcoma Unknown Not Applicable No 100% +sample TCL01-OS2.4 TCL01-OS2.4 Cell Line Malignant Primary Tumor Cell Line Humerus Not Applicable Osteosarcoma Unknown Not Applicable No 100% +sample TCL01-OSA8 TCL01-OSA8 Cell Line Malignant Primary Tumor Cell Line Humerus Not Applicable Osteosarcoma Unknown Not Applicable No 100% +sample TCL01-Vogel TCL01-Vogel Cell Line Malignant Primary Tumor Cell Line Bone Not Applicable Osteosarcoma Unknown Not Applicable No 100% +sample TCL01-STSA-1 TCL01-STSA-1 Cell Line Malignant Primary Tumor Cell Line Carpus Not Applicable Soft Tissue Sarcoma 2 Not Applicable No 100% +sample TCL01-CTAC TCL01-CTAC Cell Line Malignant Primary Tumor Cell Line Thyroid Gland Not Applicable Carcinoma Unknown 4/6/1961 Not Applicable No 100% +sample TCL01-N-1344 TCL01-N-1344 Whole Blood Not Applicable Not Applicable Whole Blood Blood Not Applicable Not Applicable Not Applicable 1/18/2011 EDTA No Not Applicable +sample TCL01-N-1866 TCL01-N-1866 Whole Blood Not Applicable Not Applicable Whole Blood Blood Not Applicable Not Applicable Not Applicable 9/30/2014 EDTA No Not Applicable +sample TCL01-N-1146 TCL01-N-1146 Whole Blood Not Applicable Not Applicable Whole Blood Blood Not Applicable Not Applicable Not Applicable 5/5/2009 EDTA No Not Applicable +sample TCL01-N-1776 TCL01-N-1776 Whole Blood Not Applicable Not Applicable Whole Blood Blood Not Applicable Not Applicable Not Applicable 6/12/2014 EDTA No Not Applicable +sample TCL01-N-353 TCL01-N-353 Tissue Normal Not Applicable Normal Tissue Skin Not Applicable Not Applicable Not Applicable 9/22/2005 Snap Frozen No Not Applicable +sample TCL01-N-166408 TCL01-N-166408 Tissue Normal Not Applicable Normal Tissue Unknown Not Applicable Not Applicable Not Applicable 5/26/2000 Snap Frozen No Not Applicable +sample TCL01-N-172160 TCL01-N-172160 Tissue Normal Not Applicable Normal Tissue Muscle Not Applicable Not Applicable Not Applicable 6/4/1999 Snap Frozen No Not Applicable +sample TCL01-N-Bella TCL01-N-Bella Whole Blood Not Applicable Not Applicable Whole Blood Blood Not Applicable Not Applicable Not Applicable 3/27/2017 EDTA No Not Applicable +sample TCL01-N-Zada TCL01-N-Zada Whole Blood Not Applicable Not Applicable Whole Blood Blood Not Applicable Not Applicable Not Applicable 2/2/2017 EDTA No Not Applicable +sample TCL01-N-CSU7 TCL01-N-CSU7 Whole Blood Not Applicable Not Applicable Whole Blood Blood Not Applicable Not Applicable Not Applicable 10/20/2014 EDTA No Not Applicable +sample TCL01-N-CSU9 TCL01-N-CSU9 Whole Blood Not Applicable Not Applicable Whole Blood Blood Not Applicable Not Applicable Not Applicable 10/30/2014 EDTA No Not Applicable +sample TCL01-N-VRCC3 TCL01-N-VRCC3 Whole Blood Not Applicable Not Applicable Whole Blood Blood Not Applicable Not Applicable Not Applicable 12/19/2013 EDTA No Not Applicable +sample TCL01-N-VRCC7 TCL01-N-VRCC7 Whole Blood Not Applicable Not Applicable Whole Blood Blood Not Applicable Not Applicable Not Applicable 3/27/2014 EDTA No Not Applicable diff --git a/model-desc/TCL01 Loading File Example Set/TCL01-study.txt b/model-desc/TCL01 Loading File Example Set/TCL01-study.txt new file mode 100644 index 0000000..70aa82c --- /dev/null +++ b/model-desc/TCL01 Loading File Example Set/TCL01-study.txt @@ -0,0 +1,2 @@ +type program.program_acronym clinical_study_id clinical_study_designation clinical_study_name clinical_study_description clinical_study_type date_of_iacuc_approval dates_of_conduct accession_id study_disposition +study CMCP Cell Line WES TCL01 Whole exome sequencing analysis of canine cancer cell lines "Cancer cell lines have been used for drug sensitivity assays in cancer research for decades. Recent sequencing analyses have shown that mutational profiles of human cancer cell lines often correlate with oncogene addiction and drug sensitivity. To identify somatic variants that contribute to pathogenesis and therapeutic sensitivity, this study analyzed whole exome sequencing of 33 established cancer cell lines from 10 cancer types. The study results identified 61 candidate cancer drivers across 30 cell lines. The most frequently mutated cancer driver was TP53 with 15 mutations in 12 cell lines. Additionally, 12 cell lines were sensitive to MEK1/2 inhibitor, trametinib, and exhibited constitutive or serum-activated ERK1/2 phosphorylation, and 8 carried MAPK pathway cancer driver variants in NF1, BRAF, N/KRAS genes." 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Sequence Analysis Files.tsv b/model-desc/TCL01 Loading File Example Set/TCL01-File_Transfer_Manifest - Sequence Analysis Files.tsv deleted file mode 100644 index 6af23b6..0000000 --- a/model-desc/TCL01 Loading File Example Set/TCL01-File_Transfer_Manifest - Sequence Analysis Files.tsv +++ /dev/null @@ -1,93 +0,0 @@ -type sample.sample_id file_name file_type file_description original_file_size original_md5sum -file TCL01-17-71 1771_recal_reads.bai Index File tumor cell line sample, TCL01-17-71: bam index of WES reads 6193232 09ed1edc79ec99b73833b08833ee401f -file TCL01-17-71 1771_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-17-71: WES reads to CanFam3.1 15575029136 8bafe042b0763e32b45ba2c0b9b080fe -file TCL01-17CM98 17CM98_recal_reads.bai Index File tumor cell line sample, TCL01-17CM98: bam index of WES reads 6154544 9c3b9c02db8d16dc0796e77ec36c802b -file TCL01-17CM98 17CM98_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-17CM98: WES reads to CanFam3.1 15935376497 c480c22d6eb7560b1e406767fc7069bb -file TCL01-Abrams ABRAMS_recal_reads.bai Index File tumor cell line sample, TCL01-Abrams: bam index of WES reads 6129784 7eaac5b155f96e16af9545e456244e29 -file TCL01-Abrams ABRAMS_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-Abrams: WES reads to CanFam3.1 14521128290 679600426205d8a7bf5e98cf26a4e6b1 -file TCL01-Angus ANGUS_recal_reads.bai Index File tumor cell line sample, TCL01-Angus: bam index of WES reads 6007608 cd8d7f8babd7c827acf63809c6000b83 -file TCL01-Angus ANGUS_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-Angus: WES reads to CanFam3.1 12309776649 a91d206c8d7612143f350d03f559a717 -file TCL01-Bliley BLILEY_recal_reads.bai Index File tumor cell line sample, TCL01-Bliley: bam index of WES reads 6190512 083f20373c0274ce6908276abb980360 -file TCL01-Bliley BLILEY_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-Bliley: WES reads to CanFam3.1 12379230451 eb7fb184c629ef4a7cbd1062c39adefe -file TCL01-BRMCT BRMCT_recal_reads.bai Index File tumor cell line sample, TCL01-BRMCT: bam index of WES reads 5993984 75a569264267e649c6f673593d227f2e -file TCL01-BRMCT BRMCT_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-BRMCT: WES reads to CanFam3.1 12734958795 7dd610733ab4a545ed180b839557d742 -file TCL01-C2 C2_recal_reads.bai Index File tumor cell line sample, TCL01-C2: bam index of WES reads 5952792 bcb37314c12165b79fff0af32b954e2d -file TCL01-C2 C2_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-C2: WES reads to CanFam3.1 14206860537 2732ae20e0d04330ff8d6dcae56fc541 -file TCL01-Cindy CINDY_recal_reads.bai Index File tumor cell line sample, TCL01-Cindy: bam index of WES reads 6045320 70f7cb898b5bc9dae2a6e0f776d2f25e -file TCL01-Cindy CINDY_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-Cindy: WES reads to CanFam3.1 11321375167 b5315f52dd138f64408d0b2717827be7 -file TCL01-CLBL1 CLBL1_recal_reads.bai Index File tumor cell line sample, TCL01-CLBL1: bam index of WES reads 6089344 91f881d13abc07ecb2a9acda49ec6592 -file TCL01-CLBL1 CLBL1_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-CLBL1: WES reads to CanFam3.1 12879642030 2b703e160fd67bd600bc06c4e5194dbc -file TCL01-CLL-1390 CLL1390_recal_reads.bai Index File tumor cell line sample, TCL01-CLL-1390: bam index of WES reads 5940688 6f981ad147ca14172d90bb71ee2d6b47 -file TCL01-CLL-1390 CLL1390_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-CLL-1390: WES reads to CanFam3.1 11063183792 6e5f2d1b70e1a15aa8161d8ff08b4f3c -file TCL01-CML-6M CML6M_recal_reads.bai Index File tumor cell line sample, TCL01-CML-6M: bam index of WES reads 6017352 fd4f31e0639812fc9720eec8c1eaab5e -file TCL01-CML-6M CML6M_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-CML-6M: WES reads to CanFam3.1 13819912565 ff81883bb52db4529684baf9d08f0d47 -file TCL01-CML-10C2 CML8410C2_recal_reads.bai Index File tumor cell line sample, TCL01-CML-10C2: bam index of WES reads 5775352 c768ea54e7d2582abfc0e879a56e64bd -file TCL01-CML-10C2 CML8410C2_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-CML-10C2: WES reads to CanFam3.1 11547785491 341d0de70c749743ba302224523bb282 -file TCL01-CMT12 CMT12_recal_reads.bai Index File tumor cell line sample, TCL01-CMT12: bam index of WES reads 5861768 f3c6e5275164b4bd169d48ca3eccc8c9 -file TCL01-CMT12 CMT12_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-CMT12: WES reads to CanFam3.1 11503041279 3674662154f40c618800e00fe1a01cff -file TCL01-CTAC CTAC_recal_reads.bai Index File tumor cell line sample, TCL01-CTAC: bam index of WES reads 5967232 000acc71589ef0f0651b6568f74db029 -file TCL01-CTAC CTAC_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-CTAC: WES reads to CanFam3.1 12333386882 f820e4a1903de38de47032daabd368be -file TCL01-D-17 D17_recal_reads.bai Index File tumor cell line sample, TCL01-D-17: bam index of WES reads 6167080 65b6e7f9863ac7702245aec0ace69bec -file TCL01-D-17 D17_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-D-17: WES reads to CanFam3.1 14885423514 743f1238a56a582ea3b368ab28e1429f -file TCL01-DEN-HSA DENNY_recal_reads.bai Index File tumor cell line sample, TCL01-DEN-HSA: bam index of WES reads 6009952 580df4374c123151ce6c6b9c9502ca5a -file TCL01-DEN-HSA DENNY_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-DEN-HSA: WES reads to CanFam3.1 11416481531 62e9ca8c6c9a8dbf56a06fb63e433be4 -file TCL01-DH82 DH82_recal_reads.bai Index File tumor cell line sample, TCL01-DH82: bam index of WES reads 6038128 89a41178d5b5f36a6c4a25c3d4b67348 -file TCL01-DH82 DH82_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-DH82: WES reads to CanFam3.1 15276960482 7a4be07d1e8558140d0fd98eff7b9a0f -file TCL01-Gracie GRACIE_recal_reads.bai Index File tumor cell line sample, TCL01-Gracie: bam index of WES reads 6272816 9ab3f467c8ff7be49da8110672e93b1a -file TCL01-Gracie GRACIE_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-Gracie: WES reads to CanFam3.1 20107363220 c1d290ecf6391f5eff97b0fb509e2fe7 -file TCL01-HMPOS HMPOS_recal_reads.bai Index File tumor cell line sample, TCL01-HMPOS: bam index of WES reads 5922504 9dd5edeef4f8ea4b31e3e467e309f58b -file TCL01-HMPOS HMPOS_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-HMPOS: WES reads to CanFam3.1 13004970608 fde03039d6d2e640928f5393c12a5ed6 -file TCL01-Jones JONES_recal_reads.bai Index File tumor cell line sample, TCL01-Jones: bam index of WES reads 6019640 4ca1cf7a0ec588a521bd2639a42030c7 -file TCL01-Jones JONES_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-Jones: WES reads to CanFam3.1 15484551373 b209406b089ff9e6c214815028205e03 -file TCL01-Kinsey KINSEY_recal_reads.bai Index File tumor cell line sample, TCL01-Kinsey: bam index of WES reads 6002392 c9a9d5a198b71b82ece903a071e412c3 -file TCL01-Kinsey KINSEY_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-Kinsey: WES reads to CanFam3.1 13028953715 64fb3640a3d8c83ef9c55c6d988a9f0b -file TCL01-McKinley MACKINLEY_recal_reads.bai Index File tumor cell line sample, TCL01-McKinley: bam index of WES reads 5991712 5da19e58266a35086cf252f4744f93e6 -file TCL01-McKinley MACKINLEY_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-McKinley: WES reads to CanFam3.1 15930203963 df11b00c83de825d262417103d364e1a -file TCL01-Moresco MORESCO_recal_reads.bai Index File tumor cell line sample, TCL01-Moresco: bam index of WES reads 5980688 f93ca8cd177eabad0e7f9c79c035f9e9 -file TCL01-Moresco MORESCO_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-Moresco: WES reads to CanFam3.1 12969130310 f5d91b56967b5375331410912c54dcc8 -file TCL01-Nike NIKE_recal_reads.bai Index File tumor cell line sample, TCL01-Nike: bam index of WES reads 5982416 3b6917d9ea7ae9e4f35980bf3b60a88e -file TCL01-Nike NIKE_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-Nike: WES reads to CanFam3.1 13834591537 757ff28e42b24d2261179bccbf696f14 -file TCL01-OS2.4 OS2-4_recal_reads.bai Index File tumor cell line sample, TCL01-OS2.4: bam index of WES reads 6132328 7d3b98a5789bf9270e3292fae787f60b -file TCL01-OS2.4 OS2-4_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-OS2.4: WES reads to CanFam3.1 16406343532 d31aeeb6f44600c36cc3838bfc4c8af6 -file TCL01-OSA8 OSA8_recal_reads.bai Index File tumor cell line sample, TCL01-OSA8: bam index of WES reads 6169168 6de0d625b4c9995c39c0e6fcd3c79e9b -file TCL01-OSA8 OSA8_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-OSA8: WES reads to CanFam3.1 15295197872 b3dbc062e48c7db29596e25f90b3bc7a -file TCL01-OSW OSW_recal_reads.bai Index File tumor cell line sample, TCL01-OSW: bam index of WES reads 6129712 fe2a0df060c8d40be92ef0e835255df4 -file TCL01-OSW OSW_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-OSW: WES reads to CanFam3.1 15645298941 b7a0879015e0b583e4a20a54ab08abeb -file TCL01-Parks PARKS_recal_reads.bai Index File tumor cell line sample, TCL01-Parks: bam index of WES reads 6534840 2b466cafddc7b428ff05da1a15dc6cf6 -file TCL01-Parks PARKS_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-Parks: WES reads to CanFam3.1 20117760429 34d6fdeef92bbf19b6887f0b7752116a -file TCL01-SB SB_recal_reads.bai Index File tumor cell line sample, TCL01-SB: bam index of WES reads 6173640 8f4fc8218a773798b81d1573b811c8da -file TCL01-SB SB_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-SB: WES reads to CanFam3.1 15742684377 f8f253afb557f0e33a0a864a4d862e7b -file TCL01-STSA-1 STS-1_recal_reads.bai Index File tumor cell line sample, TCL01-STSA-1: bam index of WES reads 6178592 09abe8721e1603d86e8286eff9d24d87 -file TCL01-STSA-1 STS-1_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-STSA-1: WES reads to CanFam3.1 16771819055 c4ce1f8bcc879a4838a81ea5e8843be9 -file TCL01-Tyler1 TYLER1_recal_reads.bai Index File tumor cell line sample, TCL01-Tyler1: bam index of WES reads 5936288 3ab276af9b2f8dcf8abba7af49c954a6 -file TCL01-Tyler1 TYLER1_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-Tyler1: WES reads to CanFam3.1 11471388290 2f3a05cd811bfeb115f3b897cec6a12b -file TCL01-Tyler2 TYLER2_recal_reads.bai Index File tumor cell line sample, TCL01-Tyler2: bam index of WES reads 6128568 fc354a42685615be86e35d4d1018239e -file TCL01-Tyler2 TYLER2_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-Tyler2: WES reads to CanFam3.1 15424341682 fd54a81f8508833a966b241293793218 -file TCL01-Vogel VOGEL_recal_reads.bai Index File tumor cell line sample, TCL01-Vogel: bam index of WES reads 6059208 9b5111bd59cadff5c0cc00c3182b5334 -file TCL01-Vogel VOGEL_recal_reads.bam Whole Exome Sequence File tumor cell line sample, TCL01-Vogel: WES reads to CanFam3.1 22941297095 5a33ed689898579edde9ab4bf7ac6d17 -file TCL01-N-1146 N-1146_recal_reads.bai Index File normal sample, TCL01-N-1146: bam index of WES reads 5966640 871146c4742be026a8845a1eacf7120d -file TCL01-N-1146 N-1146_recal_reads.bam Whole Exome Sequence File normal sample, TCL01-N-1146: WES reads to CanFam3.1 13709569910 c6f0a5dcfaf8b52b0b9c30df72511c26 -file TCL01-N-1344 N-1344_recal_reads.bai Index File normal sample, TCL01-N-1344: bam index of WES reads 5483208 3bb1c7b36476ea8825a67506e3dbbe2d -file TCL01-N-1344 N-1344_recal_reads.bam Whole Exome Sequence File normal sample, TCL01-N-1344: WES reads to CanFam3.1 8496493381 52c6830d322d10c226e62a03be03aca4 -file TCL01-N-166408 N-166408_recal_reads.bai Index File normal sample, TCL01-N-166408: bam index of WES reads 5435520 43d7c317a765880bfc6c187dde17f620 -file TCL01-N-166408 N-166408_recal_reads.bam Whole Exome Sequence File normal sample, TCL01-N-166408: WES reads to CanFam3.1 9536035091 e08b87efd448b31115f0b854d2778cfd -file TCL01-N-172160 N-172160_recal_reads.bai Index File normal sample, TCL01-N-172160: bam index of WES reads 5588544 ed073737170ed2a5972e979074f6d80f -file TCL01-N-172160 N-172160_recal_reads.bam Whole Exome Sequence File normal sample, TCL01-N-172160: WES reads to CanFam3.1 8806593257 1ab700451aa54c8f36495fc852c50807 -file TCL01-N-1776 N-1776_recal_reads.bai Index File normal sample, TCL01-N-1776: bam index of WES reads 5632672 f7e0e0e15ed30c96abe9a7ca932d48a8 -file TCL01-N-1776 N-1776_recal_reads.bam Whole Exome Sequence File normal sample, TCL01-N-1776: WES reads to CanFam3.1 9211871132 93f70d106718812541d0cc9b9b2a3f5e -file TCL01-N-1866 N-1866_recal_reads.bai Index File normal sample, TCL01-N-1866: bam index of WES reads 5817080 f6206908d6f88ad46ad0dd29a7520da4 -file TCL01-N-1866 N-1866_recal_reads.bam Whole Exome Sequence File normal sample, TCL01-N-1866: WES reads to CanFam3.1 11810859656 5a9937c8d6143eca6bd77de6699a7817 -file TCL01-N-353 N-353_recal_reads.bai Index File normal sample, TCL01-N-353: bam index of WES reads 5572704 bfc15de56f00eb38c7fa96a43ea6d57f -file TCL01-N-353 N-353_recal_reads.bam Whole Exome Sequence File normal sample, TCL01-N-353: WES reads to CanFam3.1 8616102202 3c7e5c329e781b192e0b804ba5fc94f6 -file TCL01-N-Bella N-Bella_recal_reads.bai Index File normal sample, TCL01-N-Bella: bam index of WES reads 5677384 29e49563d47e23d946a1bb0516c489cc -file TCL01-N-Bella N-Bella_recal_reads.bam Whole Exome Sequence File normal sample, TCL01-N-Bella: WES reads to CanFam3.1 12052962019 34b250eed7221d0b53b6f425208f3651 -file TCL01-N-CSU7 N-csu7_recal_reads.bai Index File normal sample, TCL01-N-CSU7: bam index of WES reads 5658952 bb0d4e4867d234bf5ef04c59d97726ad -file TCL01-N-CSU7 N-csu7_recal_reads.bam Whole Exome Sequence File normal sample, TCL01-N-CSU7: WES reads to CanFam3.1 13349785456 ecf5dd62861abf5f12b678ef4a9a7211 -file TCL01-N-CSU9 N-CSU9_recal_reads.bai Index File normal sample, TCL01-N-CSU9: bam index of WES reads 5544840 a62599e81a72d19b6d4640b6516bcae5 -file TCL01-N-CSU9 N-CSU9_recal_reads.bam Whole Exome Sequence File normal sample, TCL01-N-CSU9: WES reads to CanFam3.1 12055125754 0337180cffbc95e501f4c49289068d73 -file TCL01-N-VRCC3 N-vrcc3_recal_reads.bai Index File normal sample, TCL01-N-VRCC3: bam index of WES reads 5605400 2164cc3caf1d69ba3a5acaae222b13e1 -file TCL01-N-VRCC3 N-vrcc3_recal_reads.bam Whole Exome Sequence File normal sample, TCL01-N-VRCC3: WES reads to CanFam3.1 12165094093 8ea6e5e94b251c1bbc3c121f26646095 -file TCL01-N-VRCC7 N-VRCC7_recal_reads.bai Index File normal sample, TCL01-N-VRCC7: bam index of WES reads 5559040 505553c39256f2db02776a8d332ffdfc -file TCL01-N-VRCC7 N-VRCC7_recal_reads.bam Whole Exome Sequence File normal sample, TCL01-N-VRCC7: WES reads to CanFam3.1 11179218619 921b99b5ba416713c76c4be9e32f1399 -file TCL01-N-Zada N-Zada_recal_reads.bai Index File normal sample, TCL01-N-Zada: bam index of WES reads 5518024 b3e1f7a993369723c4e5763131425b84 -file TCL01-N-Zada N-Zada_recal_reads.bam Whole Exome Sequence File normal sample, TCL01-N-Zada: WES reads to CanFam3.1 11175904110 c92d6de4ae3bc347604fc6a3eb29ee05 diff --git a/model-desc/TCL01 Loading File Example Set/TCL01-File_Transfer_Manifest - Study Files.tsv b/model-desc/TCL01 Loading File Example Set/TCL01-File_Transfer_Manifest - Study Files.tsv deleted file mode 100644 index f862295..0000000 --- a/model-desc/TCL01 Loading File Example Set/TCL01-File_Transfer_Manifest - Study Files.tsv +++ /dev/null @@ -1,4 +0,0 @@ -"type" " case.case_id" " study.clinical_study_designation" " sample.sample_id" " diagnosis.diagnosis_id" "file_name" "file_type" "file_description" "original_file_size" "original_md5sum" -"file" "TCL01" "TCL01_CellLine_CDS_Variants.csv" "Supplemental Data File" "Cell line coding region somatic variants " 4173475 "b6cb025a2062a8f88f17e6314e6be44c" -"file" "TCL01" "TCL01_CellLineSourcing_STRs_DrugSensitivity.xlsx" "Supplemental Data File" "Cell line sourcing data, STR analysis, and drug sensitivity assay" 41862 "fc07413be62d11ff99ad33899b6fbfe7" -"file" "TCL01" "TCL01_Study_Protocol.docx" "Study Protocol" "Background, methods, and key results" 219492 "148ab1ba4faf414842cbf64750cd3a7a" diff --git a/model-desc/TCL01 Loading File Example Set/TCL01-case.txt b/model-desc/TCL01 Loading File Example Set/TCL01-case.txt deleted file mode 100644 index 7480c05..0000000 --- a/model-desc/TCL01 Loading File Example Set/TCL01-case.txt +++ /dev/null @@ -1,46 +0,0 @@ -type study.clinical_study_designation case_id patient_id patient_first_name -case TCL01 TCL01-Angus Angus Angus -case TCL01 TCL01-Bliley Bliley Socks -case TCL01 TCL01-Kinsey Kinsey Kinsey -case TCL01 TCL01-Tyler Tyler Tyler -case TCL01 TCL01-Cindy Cindy Cindy -case TCL01 TCL01-DEN-HSA DEN-HSA -case TCL01 TCL01-SB SB -case TCL01 TCL01-DH82 DH82 -case TCL01 TCL01-Nike Nike Nike -case TCL01 TCL01-CLL-1390 CLL-1390 -case TCL01 TCL01-17-71 17-71 -case TCL01 TCL01-CLBL1 CLBL1 -case TCL01 TCL01-OSW OSW -case TCL01 TCL01-CMT12 CMT12 -case TCL01 TCL01-BRMCT BRMCT -case TCL01 TCL01-C2 C2 -case TCL01 TCL01-17CM98 17CM98 -case TCL01 TCL01-CML-10C2 CML-10C2 -case TCL01 TCL01-CML-6M CML-6M -case TCL01 TCL01-Jones Jones -case TCL01 TCL01-Parks Parks -case TCL01 TCL01-Abrams Abrams -case TCL01 TCL01-D-17 D-17 -case TCL01 TCL01-Gracie Gracie Gracie -case TCL01 TCL01-HMPOS HMPOS -case TCL01 TCL01-McKinley McKinley -case TCL01 TCL01-Moresco Moresco -case TCL01 TCL01-OS2.4 OS2.4 -case TCL01 TCL01-OSA8 OSA8 -case TCL01 TCL01-Vogel Vogel -case TCL01 TCL01-STSA-1 STSA-1 -case TCL01 TCL01-CTAC CTAC -case TCL01 TCL01-N-1344 N-1344 -case TCL01 TCL01-N-1866 N-1866 -case TCL01 TCL01-N-1146 N-1146 -case TCL01 TCL01-N-1776 N-1776 -case TCL01 TCL01-N-353 N-353 -case TCL01 TCL01-N-166408 N-166408 -case TCL01 TCL01-N-172160 N-172160 -case TCL01 TCL01-N-Bella N-Bella Bella -case TCL01 TCL01-N-Zada N-Zada Zada -case TCL01 TCL01-N-CSU7 N-CSU7 -case TCL01 TCL01-N-CSU9 N-CSU9 -case TCL01 TCL01-N-VRCC3 N-VRCC3 -case TCL01 TCL01-N-VRCC7 N-VRCC7 diff --git a/model-desc/TCL01 Loading File Example Set/TCL01-demographic.txt b/model-desc/TCL01 Loading File Example Set/TCL01-demographic.txt deleted file mode 100644 index f5ae627..0000000 --- a/model-desc/TCL01 Loading File Example Set/TCL01-demographic.txt +++ /dev/null @@ -1,46 +0,0 @@ -type case.case_id demographic_id breed patient_age_at_enrollment sex neutered_indicator weight -demographic TCL01-Angus TCL01-Angus Scottish Terrier Male Unknown -demographic TCL01-Bliley TCL01-Bliley Basenji 10 Female Yes 17 -demographic TCL01-Kinsey TCL01-Kinsey Australian Shepherd Unknown Unknown -demographic TCL01-Tyler TCL01-Tyler Beagle 8 Male Yes -demographic TCL01-Cindy TCL01-Cindy Labrador Retriever 3 Female Unknown -demographic TCL01-DEN-HSA TCL01-DEN-HSA Golden Retriever 11 Male Yes -demographic TCL01-SB TCL01-SB German Shepherd Dog 9 Male Unknown -demographic TCL01-DH82 TCL01-DH82 Golden Retriever 10 Male No -demographic TCL01-Nike TCL01-Nike Unknown Unknown Unknown -demographic TCL01-CLL-1390 TCL01-CLL-1390 Unknown Unknown Unknown -demographic TCL01-17-71 TCL01-17-71 Unknown Unknown Unknown -demographic TCL01-CLBL1 TCL01-CLBL1 Bernese Mountain Dog 8 Male Unknown -demographic TCL01-OSW TCL01-OSW Airedale Terrier 5.5 Male Unknown -demographic TCL01-CMT12 TCL01-CMT12 Poodle Female Unknown -demographic TCL01-BRMCT TCL01-BRMCT Unknown Unknown Unknown -demographic TCL01-C2 TCL01-C2 Unknown Female Unknown -demographic TCL01-17CM98 TCL01-17CM98 Unknown Unknown Unknown -demographic TCL01-CML-10C2 TCL01-CML-10C2 Unknown Unknown Unknown -demographic TCL01-CML-6M TCL01-CML-6M Mixed Breed 8 Unknown Unknown -demographic TCL01-Jones TCL01-Jones Miniature Dachshund 14 Female Yes 6.2 -demographic TCL01-Parks TCL01-Parks Labrador Retriever 12 Female Yes 32 -demographic TCL01-Abrams TCL01-Abrams Rottweiler 2.5 Male Unknown 40.8 -demographic TCL01-D-17 TCL01-D-17 Poodle 11 Female Unknown -demographic TCL01-Gracie TCL01-Gracie Unknown Unknown Unknown -demographic TCL01-HMPOS TCL01-HMPOS Mixed Breed 1.5 Male Unknown -demographic TCL01-McKinley TCL01-McKinley Unknown Unknown Unknown -demographic TCL01-Moresco TCL01-Moresco Unknown Unknown Unknown -demographic TCL01-OS2.4 TCL01-OS2.4 Golden Retriever 5 Unknown Unknown -demographic TCL01-OSA8 TCL01-OSA8 Rottweiler 2 Male Unknown -demographic TCL01-Vogel TCL01-Vogel Unknown Unknown Unknown -demographic TCL01-STSA-1 TCL01-STSA-1 Golden Retriever 7 Male Yes -demographic TCL01-CTAC TCL01-CTAC Boxer 7 Female Unknown -demographic TCL01-N-1344 TCL01-N-1344 Labrador Retriever Male Yes 42.8 -demographic TCL01-N-1866 TCL01-N-1866 Greyhound Female Yes 23.4 -demographic TCL01-N-1146 TCL01-N-1146 Bernese Mountain Dog Male Yes 47.2 -demographic TCL01-N-1776 TCL01-N-1776 Rottweiler Female Yes 36 -demographic TCL01-N-353 TCL01-N-353 Mixed Breed Male Yes 23.6 -demographic TCL01-N-166408 TCL01-N-166408 Mixed Breed Male Yes 47 -demographic TCL01-N-172160 TCL01-N-172160 Shetland Sheepdog Female Yes 16 -demographic TCL01-N-Bella TCL01-N-Bella Golden Retriever Female Yes 34 -demographic TCL01-N-Zada TCL01-N-Zada Rhodesian Ridgeback Female Yes 38.8 -demographic TCL01-N-CSU7 TCL01-N-CSU7 Golden Retriever Male Yes 27.4 -demographic TCL01-N-CSU9 TCL01-N-CSU9 Cocker Spaniel Female Yes 13.3 -demographic TCL01-N-VRCC3 TCL01-N-VRCC3 Golden Retriever Female Yes -demographic TCL01-N-VRCC7 TCL01-N-VRCC7 Boxer Female Yes diff --git a/model-desc/TCL01 Loading File Example Set/TCL01-diagnosis.txt b/model-desc/TCL01 Loading File Example Set/TCL01-diagnosis.txt deleted file mode 100644 index 0bc216f..0000000 --- a/model-desc/TCL01 Loading File Example Set/TCL01-diagnosis.txt +++ /dev/null @@ -1,46 +0,0 @@ -type case.case_id diagnosis_id disease_term primary_disease_site stage_of_disease best_response treatment_data follow_up_data pathology_report concurrent_disease concurrent_disease_type -diagnosis TCL01-Angus TCL01-Angus Bladder Cancer Unknown Unknown Not Applicable Yes No No Unknown -diagnosis TCL01-Bliley TCL01-Bliley Bladder Cancer Distal Urethra Unknown Not Applicable Yes No No No -diagnosis TCL01-Kinsey TCL01-Kinsey Bladder Cancer Unknown Unknown Not Applicable Yes No No Unknown -diagnosis TCL01-Tyler TCL01-Tyler Bladder Cancer Urethra, Prostate Unknown Not Applicable Yes No No Unknown -diagnosis TCL01-Cindy TCL01-Cindy Hemangiosarcoma Unknown Unknown Not Applicable Yes No No Unknown -diagnosis TCL01-DEN-HSA TCL01-DEN-HSA Hemangiosarcoma Kidney Unknown Not Applicable Yes No No Unknown -diagnosis TCL01-SB TCL01-SB Hemangiosarcoma Subcutis Unknown Not Applicable Yes No No Unknown -diagnosis TCL01-DH82 TCL01-DH82 Histiocytic Sarcoma Bone Marrow Unknown Not Applicable Yes No No Unknown -diagnosis TCL01-Nike TCL01-Nike Histiocytic Sarcoma Unknown Unknown Not Applicable Yes No No Unknown -diagnosis TCL01-CLL-1390 TCL01-CLL-1390 T Cell Leukemia Unknown Unknown Not Applicable Yes No No Unknown -diagnosis TCL01-17-71 TCL01-17-71 B Cell Lymphoma Lymph Node Unknown Not Applicable Yes No No Unknown -diagnosis TCL01-CLBL1 TCL01-CLBL1 B Cell Lymphoma Lymph Node Unknown Not Applicable Yes No No Unknown -diagnosis TCL01-OSW TCL01-OSW Lymphoma Pleural Cavity Unknown Not Applicable Yes No No Unknown -diagnosis TCL01-CMT12 TCL01-CMT12 Mammary Cancer Mammary Gland Unknown Not Applicable Yes No No Unknown -diagnosis TCL01-BRMCT TCL01-BRMCT Mast Cell Tumor Subcutis Unknown Not Applicable Yes No No Unknown -diagnosis TCL01-C2 TCL01-C2 Mast Cell Tumor Subcutis Unknown Not Applicable Yes No No Unknown -diagnosis TCL01-17CM98 TCL01-17CM98 Melanoma Mouth Unknown Not Applicable Yes No No Unknown -diagnosis TCL01-CML-10C2 TCL01-CML-10C2 Melanoma Skin Unknown Not Applicable Yes No No Unknown -diagnosis TCL01-CML-6M TCL01-CML-6M Melanoma Skin Unknown Not Applicable Yes No No Unknown -diagnosis TCL01-Jones TCL01-Jones Melanoma Mouth Unknown Not Applicable Yes No No Unknown -diagnosis TCL01-Parks TCL01-Parks Melanoma Mouth Unknown Not Applicable Yes No No Unknown -diagnosis TCL01-Abrams TCL01-Abrams Osteosarcoma Bone (Appendicular) Unknown Not Applicable Yes No No Unknown -diagnosis TCL01-D-17 TCL01-D-17 Osteosarcoma Bone (Appendicular) Unknown Not Applicable Yes No No Unknown -diagnosis TCL01-Gracie TCL01-Gracie Osteosarcoma Bone (Appendicular) Unknown Not Applicable Yes No No Unknown -diagnosis TCL01-HMPOS TCL01-HMPOS Osteosarcoma Bone (Appendicular) Unknown Not Applicable Yes No No Unknown -diagnosis TCL01-McKinley TCL01-McKinley Osteosarcoma Bone (Appendicular) Unknown Not Applicable Yes No No Unknown -diagnosis TCL01-Moresco TCL01-Moresco Osteosarcoma Bone (Appendicular) Unknown Not Applicable Yes No No Unknown -diagnosis TCL01-OS2.4 TCL01-OS2.4 Osteosarcoma Bone (Appendicular) Unknown Not Applicable Yes No No Unknown -diagnosis TCL01-OSA8 TCL01-OSA8 Osteosarcoma Bone (Appendicular) Unknown Not Applicable Yes No No Unknown -diagnosis TCL01-Vogel TCL01-Vogel Osteosarcoma Bone (Appendicular) Unknown Not Applicable Yes No No Unknown -diagnosis TCL01-STSA-1 TCL01-STSA-1 Soft Tissue Sarcoma Carpus Unknown Not Applicable Yes No No Unknown -diagnosis TCL01-CTAC TCL01-CTAC Thyroid Cancer Thyroid Gland Unknown Not Applicable Yes No No Unknown -diagnosis TCL01-N-1344 TCL01-N-1344 Splenic Hyperplasia Spleen Not Applicable Not Applicable No No No Unknown -diagnosis TCL01-N-1866 TCL01-N-1866 Splenic Hematoma Spleen Not Applicable Not Applicable No No No Unknown -diagnosis TCL01-N-1146 TCL01-N-1146 Lipoma Chest Wall Not Applicable Not Applicable No No No Unknown -diagnosis TCL01-N-1776 TCL01-N-1776 Fibrolipoma Shoulder Not Applicable Not Applicable No No No Unknown -diagnosis TCL01-N-353 TCL01-N-353 Bladder Cancer Bladder Unknown Not Applicable No No No Unknown -diagnosis TCL01-N-166408 TCL01-N-166408 Bladder Cancer Bladder Unknown Not Applicable No No No Unknown -diagnosis TCL01-N-172160 TCL01-N-172160 Bladder Cancer Bladder Unknown Not Applicable No No No Unknown -diagnosis TCL01-N-Bella TCL01-N-Bella B Cell Lymphoma Lymph Node Unknown Not Applicable No No No Unknown -diagnosis TCL01-N-Zada TCL01-N-Zada B Cell Lymphoma Lymph Node Unknown Not Applicable No No No Unknown -diagnosis TCL01-N-CSU7 TCL01-N-CSU7 B Cell Lymphoma Lymph Node Unknown Not Applicable No No No Unknown -diagnosis TCL01-N-CSU9 TCL01-N-CSU9 B Cell Lymphoma Lymph Node Unknown Not Applicable No No No Unknown -diagnosis TCL01-N-VRCC3 TCL01-N-VRCC3 B Cell Lymphoma Lymph Node Unknown Not Applicable No No No Unknown -diagnosis TCL01-N-VRCC7 TCL01-N-VRCC7 B Cell Lymphoma Lymph Node Unknown Not Applicable No No No Unknown diff --git a/model-desc/TCL01 Loading File Example Set/TCL01-enrollment.txt b/model-desc/TCL01 Loading File Example Set/TCL01-enrollment.txt deleted file mode 100644 index 58e7b86..0000000 --- a/model-desc/TCL01 Loading File Example Set/TCL01-enrollment.txt +++ /dev/null @@ -1,46 +0,0 @@ -type case.case_id enrollment_id site_short_name -enrollment TCL01-Angus TCL01-Angus Tufts -enrollment TCL01-Bliley TCL01-Bliley CSU -enrollment TCL01-Kinsey TCL01-Kinsey Tufts -enrollment TCL01-Tyler TCL01-Tyler Tufts -enrollment TCL01-Cindy TCL01-Cindy UI -enrollment TCL01-DEN-HSA TCL01-DEN-HSA UWM -enrollment TCL01-SB TCL01-SB UWM -enrollment TCL01-DH82 TCL01-DH82 ATCC -enrollment TCL01-Nike TCL01-Nike MSU -enrollment TCL01-CLL-1390 TCL01-CLL-1390 UCD -enrollment TCL01-17-71 TCL01-17-71 UPENN -enrollment TCL01-CLBL1 TCL01-CLBL1 Aus -enrollment TCL01-OSW TCL01-OSW OSU -enrollment TCL01-CMT12 TCL01-CMT12 AU -enrollment TCL01-BRMCT TCL01-BRMCT UCSF -enrollment TCL01-C2 TCL01-C2 UCSF -enrollment TCL01-17CM98 TCL01-17CM98 UWM -enrollment TCL01-CML-10C2 TCL01-CML-10C2 AU -enrollment TCL01-CML-6M TCL01-CML-6M AU -enrollment TCL01-Jones TCL01-Jones CSU -enrollment TCL01-Parks TCL01-Parks CSU -enrollment TCL01-Abrams TCL01-Abrams CSU/UWM -enrollment TCL01-D-17 TCL01-D-17 ATCC -enrollment TCL01-Gracie TCL01-Gracie UWM -enrollment TCL01-HMPOS TCL01-HMPOS Tokyo -enrollment TCL01-McKinley TCL01-McKinley CSU -enrollment TCL01-Moresco TCL01-Moresco UWM -enrollment TCL01-OS2.4 TCL01-OS2.4 WSU -enrollment TCL01-OSA8 TCL01-OSA8 UM -enrollment TCL01-Vogel TCL01-Vogel CSU -enrollment TCL01-STSA-1 TCL01-STSA-1 UI -enrollment TCL01-CTAC TCL01-CTAC OSU -enrollment TCL01-N-1344 TCL01-N-1344 CSU -enrollment TCL01-N-1866 TCL01-N-1866 CSU -enrollment TCL01-N-1146 TCL01-N-1146 CSU -enrollment TCL01-N-1776 TCL01-N-1776 CSU -enrollment TCL01-N-353 TCL01-N-353 CSU -enrollment TCL01-N-166408 TCL01-N-166408 CSU -enrollment TCL01-N-172160 TCL01-N-172160 CSU -enrollment TCL01-N-Bella TCL01-N-Bella CSU -enrollment TCL01-N-Zada TCL01-N-Zada CSU -enrollment TCL01-N-CSU7 TCL01-N-CSU7 CSU -enrollment TCL01-N-CSU9 TCL01-N-CSU9 CSU -enrollment TCL01-N-VRCC3 TCL01-N-VRCC3 CSU -enrollment TCL01-N-VRCC7 TCL01-N-VRCC7 CSU diff --git a/model-desc/TCL01 Loading File Example Set/TCL01-principal_investigator.txt b/model-desc/TCL01 Loading File Example Set/TCL01-principal_investigator.txt deleted file mode 100644 index 1d96ffc..0000000 --- a/model-desc/TCL01 Loading File Example Set/TCL01-principal_investigator.txt +++ /dev/null @@ -1,2 +0,0 @@ -type study.clinical_study_designation pi_first_name pi_last_name pi_middle_initial -principal_investigator TCL01 Dawn Duval L \ No newline at end of file diff --git a/model-desc/TCL01 Loading File Example Set/TCL01-publication.txt b/model-desc/TCL01 Loading File Example Set/TCL01-publication.txt deleted file mode 100644 index aeea34e..0000000 --- a/model-desc/TCL01 Loading File Example Set/TCL01-publication.txt +++ /dev/null @@ -1,2 +0,0 @@ -type study.clinical_study_designation publication_title authorship year_of_publication journal_citation digital_object_id pubmed_id -publication TCL01 Identifying Candidate Druggable Targets in Canine Cancer Cell Lines Using Whole-Exome Sequencing Das S et al 2019 Mol Cancer Ther 18 (8): 1460-1471. 10.1158/1535-7163.MCT-18-1346 31175136 \ No newline at end of file diff --git a/model-desc/TCL01 Loading File Example Set/TCL01-sample.txt b/model-desc/TCL01 Loading File Example Set/TCL01-sample.txt deleted file mode 100644 index d6128d6..0000000 --- a/model-desc/TCL01 Loading File Example Set/TCL01-sample.txt +++ /dev/null @@ -1,47 +0,0 @@ -type case.case_id sample_id physical_sample_type general_sample_pathology tumor_sample_origin summarized_sample_type sample_site sample_chronology specific_sample_pathology tumor_grade date_of_sample_collection sample_preservation necropsy_sample percentage_tumor -sample TCL01-Angus TCL01-Angus Cell Line Malignant Primary Tumor Cell Line Bladder Not Applicable Urothelial Carcinoma Unknown Not Applicable No 100% -sample TCL01-Bliley TCL01-Bliley Cell Line Malignant Primary Tumor Cell Line Distal Urethra Not Applicable Urothelial Carcinoma Unknown Not Applicable No 100% -sample TCL01-Kinsey TCL01-Kinsey Cell Line Malignant Primary Tumor Cell Line Bladder Not Applicable Urothelial Carcinoma Unknown Not Applicable No 100% -sample TCL01-Tyler TCL01-Tyler1 Cell Line Malignant Primary Tumor Cell Line Bladder Not Applicable Urothelial Carcinoma Unknown Not Applicable No 100% -sample TCL01-Tyler TCL01-Tyler2 Cell Line Malignant Primary Tumor Cell Line Bladder Not Applicable Urothelial Carcinoma Unknown Not Applicable No 100% -sample TCL01-Cindy TCL01-Cindy Cell Line Malignant Primary Tumor Cell Line Spleen Not Applicable Hemangiosarcoma Unknown Not Applicable No 100% -sample TCL01-DEN-HSA TCL01-DEN-HSA Cell Line Malignant Primary Tumor Cell Line Kidney Not Applicable Hemangiosarcoma Unknown Not Applicable No 100% -sample TCL01-SB TCL01-SB Cell Line Malignant Primary Tumor Cell Line Skin Not Applicable Hemangiosarcoma Unknown Not Applicable No 100% -sample TCL01-DH82 TCL01-DH82 Cell Line Malignant Primary Tumor Cell Line Bone Marrow Not Applicable Histiocytic Sarcoma Unknown Not Applicable Yes 100% -sample TCL01-Nike TCL01-Nike Cell Line Malignant Primary Tumor Cell Line Unknown Not Applicable Histiocytic Sarcoma Unknown Not Applicable No 100% -sample TCL01-CLL-1390 TCL01-CLL-1390 Cell Line Malignant Primary Tumor Cell Line Unknown Not Applicable Primitive T-Cell Leukemia Unknown Not Applicable No 100% -sample TCL01-17-71 TCL01-17-71 Cell Line Malignant Primary Tumor Cell Line Lymph Node Not Applicable B Cell Lymphoma Unknown Not Applicable No 100% -sample TCL01-CLBL1 TCL01-CLBL1 Cell Line Malignant Primary Tumor Cell Line Lymph Node, Popliteal Not Applicable B Cell Lymphoma Unknown Not Applicable No 100% -sample TCL01-OSW TCL01-OSW Cell Line Malignant Metastatic Tumor Cell Line (metastasis-derived) Pleural Effusion Not Applicable T Cell Lymphoma Unknown Not Applicable No 100% -sample TCL01-CMT12 TCL01-CMT12 Cell Line Malignant Primary Tumor Cell Line Mammary Gland Not Applicable Carcinoma Unknown Not Applicable No 100% -sample TCL01-BRMCT TCL01-BRMCT Cell Line Malignant Primary Tumor Cell Line Skin Not Applicable Mast Cell Tumor Unknown Not Applicable No 100% -sample TCL01-C2 TCL01-C2 Cell Line Malignant Primary Tumor Cell Line Skin Not Applicable Mast Cell Tumor Unknown Not Applicable No 100% -sample TCL01-17CM98 TCL01-17CM98 Cell Line Malignant Metastatic Tumor Cell Line (metastasis-derived) Lymph Node Not Applicable Melanoma Unknown Not Applicable No 100% -sample TCL01-CML-10C2 TCL01-CML-10C2 Cell Line Malignant Primary Tumor Cell Line Cutis Not Applicable Melanoma Unknown Not Applicable No 100% -sample TCL01-CML-6M TCL01-CML-6M Cell Line Malignant Metastatic Tumor Cell Line (metastasis-derived) Lymph Node Not Applicable Melanoma Unknown Not Applicable No 100% -sample TCL01-Jones TCL01-Jones Cell Line Malignant Unknown Tumor Cell Line Mouth Not Applicable Melanoma Unknown Not Applicable No 100% -sample TCL01-Parks TCL01-Parks Cell Line Malignant Unknown Tumor Cell Line Mouth Not Applicable Melanoma Unknown Not Applicable No 100% -sample TCL01-Abrams TCL01-Abrams Cell Line Malignant Metastatic Tumor Cell Line (metastasis-derived) Lung Not Applicable Osteosarcoma Unknown Not Applicable No 100% -sample TCL01-D-17 TCL01-D-17 Cell Line Malignant Metastatic Tumor Cell Line (metastasis-derived) Lung Not Applicable Osteosarcoma Unknown Not Applicable No 100% -sample TCL01-Gracie TCL01-Gracie Cell Line Malignant Primary Tumor Cell Line Bone Not Applicable Osteosarcoma Unknown Not Applicable No 100% -sample TCL01-HMPOS TCL01-HMPOS Cell Line Malignant Primary Tumor Cell Line Bone Not Applicable Osteosarcoma Unknown Not Applicable No 100% -sample TCL01-McKinley TCL01-McKinley Cell Line Malignant Primary Tumor Cell Line Bone Not Applicable Osteosarcoma Unknown Not Applicable No 100% -sample TCL01-Moresco TCL01-Moresco Cell Line Malignant Primary Tumor Cell Line Bone Not Applicable Osteosarcoma Unknown Not Applicable No 100% -sample TCL01-OS2.4 TCL01-OS2.4 Cell Line Malignant Primary Tumor Cell Line Humerus Not Applicable Osteosarcoma Unknown Not Applicable No 100% -sample TCL01-OSA8 TCL01-OSA8 Cell Line Malignant Primary Tumor Cell Line Humerus Not Applicable Osteosarcoma Unknown Not Applicable No 100% -sample TCL01-Vogel TCL01-Vogel Cell Line Malignant Primary Tumor Cell Line Bone Not Applicable Osteosarcoma Unknown Not Applicable No 100% -sample TCL01-STSA-1 TCL01-STSA-1 Cell Line Malignant Primary Tumor Cell Line Carpus Not Applicable Soft Tissue Sarcoma 2 Not Applicable No 100% -sample TCL01-CTAC TCL01-CTAC Cell Line Malignant Primary Tumor Cell Line Thyroid Gland Not Applicable Carcinoma Unknown 4/6/1961 Not Applicable No 100% -sample TCL01-N-1344 TCL01-N-1344 Whole Blood Not Applicable Not Applicable Whole Blood Blood Not Applicable Not Applicable Not Applicable 1/18/2011 EDTA No Not Applicable -sample TCL01-N-1866 TCL01-N-1866 Whole Blood Not Applicable Not Applicable Whole Blood Blood Not Applicable Not Applicable Not Applicable 9/30/2014 EDTA No Not Applicable -sample TCL01-N-1146 TCL01-N-1146 Whole Blood Not Applicable Not Applicable Whole Blood Blood Not Applicable Not Applicable Not Applicable 5/5/2009 EDTA No Not Applicable -sample TCL01-N-1776 TCL01-N-1776 Whole Blood Not Applicable Not Applicable Whole Blood Blood Not Applicable Not Applicable Not Applicable 6/12/2014 EDTA No Not Applicable -sample TCL01-N-353 TCL01-N-353 Tissue Normal Not Applicable Normal Tissue Skin Not Applicable Not Applicable Not Applicable 9/22/2005 Snap Frozen No Not Applicable -sample TCL01-N-166408 TCL01-N-166408 Tissue Normal Not Applicable Normal Tissue Unknown Not Applicable Not Applicable Not Applicable 5/26/2000 Snap Frozen No Not Applicable -sample TCL01-N-172160 TCL01-N-172160 Tissue Normal Not Applicable Normal Tissue Muscle Not Applicable Not Applicable Not Applicable 6/4/1999 Snap Frozen No Not Applicable -sample TCL01-N-Bella TCL01-N-Bella Whole Blood Not Applicable Not Applicable Whole Blood Blood Not Applicable Not Applicable Not Applicable 3/27/2017 EDTA No Not Applicable -sample TCL01-N-Zada TCL01-N-Zada Whole Blood Not Applicable Not Applicable Whole Blood Blood Not Applicable Not Applicable Not Applicable 2/2/2017 EDTA No Not Applicable -sample TCL01-N-CSU7 TCL01-N-CSU7 Whole Blood Not Applicable Not Applicable Whole Blood Blood Not Applicable Not Applicable Not Applicable 10/20/2014 EDTA No Not Applicable -sample TCL01-N-CSU9 TCL01-N-CSU9 Whole Blood Not Applicable Not Applicable Whole Blood Blood Not Applicable Not Applicable Not Applicable 10/30/2014 EDTA No Not Applicable -sample TCL01-N-VRCC3 TCL01-N-VRCC3 Whole Blood Not Applicable Not Applicable Whole Blood Blood Not Applicable Not Applicable Not Applicable 12/19/2013 EDTA No Not Applicable -sample TCL01-N-VRCC7 TCL01-N-VRCC7 Whole Blood Not Applicable Not Applicable Whole Blood Blood Not Applicable Not Applicable Not Applicable 3/27/2014 EDTA No Not Applicable diff --git a/model-desc/TCL01 Loading File Example Set/TCL01-study.txt b/model-desc/TCL01 Loading File Example Set/TCL01-study.txt deleted file mode 100644 index 70aa82c..0000000 --- a/model-desc/TCL01 Loading File Example Set/TCL01-study.txt +++ /dev/null @@ -1,2 +0,0 @@ -type program.program_acronym clinical_study_id clinical_study_designation clinical_study_name clinical_study_description clinical_study_type date_of_iacuc_approval dates_of_conduct accession_id study_disposition -study CMCP Cell Line WES TCL01 Whole exome sequencing analysis of canine cancer cell lines "Cancer cell lines have been used for drug sensitivity assays in cancer research for decades. Recent sequencing analyses have shown that mutational profiles of human cancer cell lines often correlate with oncogene addiction and drug sensitivity. To identify somatic variants that contribute to pathogenesis and therapeutic sensitivity, this study analyzed whole exome sequencing of 33 established cancer cell lines from 10 cancer types. The study results identified 61 candidate cancer drivers across 30 cell lines. The most frequently mutated cancer driver was TP53 with 15 mutations in 12 cell lines. Additionally, 12 cell lines were sensitive to MEK1/2 inhibitor, trametinib, and exhibited constitutive or serum-activated ERK1/2 phosphorylation, and 8 carried MAPK pathway cancer driver variants in NF1, BRAF, N/KRAS genes." Genomics 2017-2019 000008 Unrestricted \ No newline at end of file diff --git a/model-desc/Icon-DMNav.85x85.svg b/model-desc/navigator-icon.svg similarity index 100% rename from model-desc/Icon-DMNav.85x85.svg rename to model-desc/navigator-icon.svg