From 43f18277bcf05fef52cfc6416aefc39d7e102225 Mon Sep 17 00:00:00 2001 From: Orion Banks <49208907+Bankso@users.noreply.github.com> Date: Mon, 24 Jul 2023 13:08:48 -0700 Subject: [PATCH 01/15] Add 'DatasetView_id' attribute --- modules/dataset/annotationProperty.csv | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/dataset/annotationProperty.csv b/modules/dataset/annotationProperty.csv index 89308e5..ee044e9 100644 --- a/modules/dataset/annotationProperty.csv +++ b/modules/dataset/annotationProperty.csv @@ -14,3 +14,4 @@ Dataset Grant,"Datasets associated with a grant, joined by uuids from the datase Dataset View,The denormalized manifest for dataset submission.,,"Component, Dataset Pubmed Id, Dataset Grant Number, Dataset Name, Dataset Alias, Dataset Description, Dataset Design, Dataset Assay, Dataset Species, Dataset Tumor Type, Dataset Tissue, Dataset Url, Dataset File Formats",FALSE,,,"Publication, Grant, Dataset",, Dataset Grant Number,"Grant number(s) associated with the dataset's development. Multiple values permitted, comma separated.","Affiliated/Non-Grant Associated, CA184897, CA184898, CA188388, CA193313, CA193417, CA193419, CA193461, CA193489, CA195469, CA199315, CA202123, CA202144, CA202177, CA202229, CA202241, CA209891, CA209923, CA209971, CA209975, CA209978, CA209988, CA209992, CA209997, CA210152, CA210173, CA210180, CA210181, CA210184, CA210190, CA214282, CA214292, CA214297, CA214300, CA214354, CA214369, CA214381, CA214411, CA215709, CA215794, CA215798, CA215845, CA215848, CA217297, CA217376, CA217377, CA217378, CA217450, CA217456, CA217514, CA217613, CA217617, CA217655, CA220378, CA223976, CA224012, CA224013, CA224044, CA225088, CA225566, CA227136, CA227544, CA227550, CA228608, CA228963, CA231978, CA232137, CA232161, CA232209, CA232216, CA232382, CA232517, CA234787, CA235747, CA238475, CA238720, CA238728, CA240301, CA241137, CA241927, CA243004, CA243007, CA243072, CA243073, CA243075, CA244100, CA244101, CA244107, CA244109, CA245313, CA248890, CA249799, CA250040, CA250044, CA250046, CA250481, CA251443, CA253248, CA253472, CA253540, CA253547, CA253553, CA254200, CA254886, CA256054, CA256481, CA260432, CA261694, CA261701, CA261717, CA261719, CA261822, CA261841, CA261842, CA263001, CA264583, CA264610, CA264611, CA264620, CA267170, CA268069, CA268072, CA268083, CA268084, CA271273, CA274492, CA274494, CA274499, CA274502, CA274509, CA275808",,TRUE,,,,,list like Dataset Pubmed Id,"The PubMed identifer(s) associated with the development of the dataset. Multiple values permitted, comma separated.",,,TRUE,,,,,list like +DatasetView_id,A unique primary key that enables record updates using schematic.,,,TRUE,,,,,unique From a10d7a6e0644d47c0568e79177670f22a885c8f7 Mon Sep 17 00:00:00 2001 From: Orion Banks <49208907+Bankso@users.noreply.github.com> Date: Mon, 24 Jul 2023 13:10:43 -0700 Subject: [PATCH 02/15] Add 'DatasetView_id' attribute to 'DatasetView' schema --- modules/dataset/annotationProperty.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/dataset/annotationProperty.csv b/modules/dataset/annotationProperty.csv index ee044e9..3e9d126 100644 --- a/modules/dataset/annotationProperty.csv +++ b/modules/dataset/annotationProperty.csv @@ -11,7 +11,7 @@ Dataset Tumor Type,"The tumor type(s), if applicable, of the data collected on. Dataset Tissue,"Tissue type(s) associated with the dataset. Multiple values permitted, comma separated.","Gonad, Abdominal Esophagus, Adipose Tissue, Adrenal Gland, Alveolus, Aorta, Artery, Ascending Colon, Bile Duct, Bladder, Blood, Blood Vessel, Bone, Bone Marrow, Brain, Breast, Caecum, Cancer-Associated Fibroblast, Cardia, Cartilage, Cervix Uteri, Choroid, Colon, Connective and Soft Tissue, Cornea, Duodenum, Ear, Embryo, Embryonic Heart, Endocervix, Endometrium, Endothelium, Epithelium, Esophagus, Eye, Fallopian Tube, Foreskin, Frontal Lobe, Gastroesophageal Junction, Gastrointestinal Tract, Genitourinary, Hair Follicle, Head and Neck, Heart, Heart Muscle, Hematopoietic System, Hippocampus, Intestine, Intra-Abdominal Lymph Nodes, Intrathoracic Lymph Nodes, Joint, Kidney, Larynx, Ligament, Liver, Lung, Lymph, Lymph Node, Lymph Nodes of Axilla or Arm, Lymph Nodes of Inguinal Region or Leg, Lymphatic System, Lymphoid Tissue, Main Bronchus, Mammary Gland, Meninges, Mesenchyme, Mucosa, Muscle, Nasal Cavity, Nervous System, Not Applicable, Olfactory Mucosa, Omentum, Oral Cavity, Oral Mucosa, Ovary, Pancreas, Pelvic Lymph Nodes, Pending Annotation, Periodontal Ligament, Peripheral Nerves, Peritoneum, Pharynx, Pituitary Gland, Placenta, Pleura, Prostate Gland, Rectum, Reproductive System, Respiratory System, Salivary Gland, Sclera, Sinonasal Tract, Skin, Small Intestine, Spinal Cord, Spleen, Stomach, Synovial Membrane, Tendon, Testis, Thymus, Thyroid Gland, Tongue, Tonsil, Trachea, Umbilical Cord, Unspecified, Uterus, Vagina, Vascular Endothelium, Vein, Vertebra, Peripheral Blood Mononuclear Cell",,TRUE,,,,,list like Dataset File Formats,"A list of file formats associated with the dataset. Multiple values permitted, comma separated.","AVI, BAI, BAM, BED, CDS, CHP, COOL, CSV, DB, DS_Store, FASTA, FASTQ, FCS, FIG, FREQ, GCG, GCT, GCTx, GFF3, GTF, GZIP Format, HDF, HDF5, HTML, IDAT, JPG, JSON, LIF, MAP, MAT, MATLAB script, MSF, MTX, PDF, PNG, PZFX, Python Script, R File Format, RAW, RDS, ROUT, RPROJ, RTF, SGI, SRA, STAT, TAR Format, TDF, TIFF, TSV, TXT, VCF, WIG, XML, ZIP, bed12, bedgraph, cel, cloupe, docx, mzIdentML, mzXML, pptx, rcc, xls, xlsx, MGF, BIGWIG, H5AD, H5, SF, PKL, BPM, Unspecified, Pending Annotation",,FALSE,,,,,list like Dataset Grant,"Datasets associated with a grant, joined by uuids from the dataset and grant table.",,"Component. Dataset, Grant",FALSE,,,"Dataset, Grant",, -Dataset View,The denormalized manifest for dataset submission.,,"Component, Dataset Pubmed Id, Dataset Grant Number, Dataset Name, Dataset Alias, Dataset Description, Dataset Design, Dataset Assay, Dataset Species, Dataset Tumor Type, Dataset Tissue, Dataset Url, Dataset File Formats",FALSE,,,"Publication, Grant, Dataset",, +Dataset View,The denormalized manifest for dataset submission.,,"Component, DatasetView_id, Dataset Pubmed Id, Dataset Grant Number, Dataset Name, Dataset Alias, Dataset Description, Dataset Design, Dataset Assay, Dataset Species, Dataset Tumor Type, Dataset Tissue, Dataset Url, Dataset File Formats",FALSE,,,"Publication, Grant, Dataset",, Dataset Grant Number,"Grant number(s) associated with the dataset's development. Multiple values permitted, comma separated.","Affiliated/Non-Grant Associated, CA184897, CA184898, CA188388, CA193313, CA193417, CA193419, CA193461, CA193489, CA195469, CA199315, CA202123, CA202144, CA202177, CA202229, CA202241, CA209891, CA209923, CA209971, CA209975, CA209978, CA209988, CA209992, CA209997, CA210152, CA210173, CA210180, CA210181, CA210184, CA210190, CA214282, CA214292, CA214297, CA214300, CA214354, CA214369, CA214381, CA214411, CA215709, CA215794, CA215798, CA215845, CA215848, CA217297, CA217376, CA217377, CA217378, CA217450, CA217456, CA217514, CA217613, CA217617, CA217655, CA220378, CA223976, CA224012, CA224013, CA224044, CA225088, CA225566, CA227136, CA227544, CA227550, CA228608, CA228963, CA231978, CA232137, CA232161, CA232209, CA232216, CA232382, CA232517, CA234787, CA235747, CA238475, CA238720, CA238728, CA240301, CA241137, CA241927, CA243004, CA243007, CA243072, CA243073, CA243075, CA244100, CA244101, CA244107, CA244109, CA245313, CA248890, CA249799, CA250040, CA250044, CA250046, CA250481, CA251443, CA253248, CA253472, CA253540, CA253547, CA253553, CA254200, CA254886, CA256054, CA256481, CA260432, CA261694, CA261701, CA261717, CA261719, CA261822, CA261841, CA261842, CA263001, CA264583, CA264610, CA264611, CA264620, CA267170, CA268069, CA268072, CA268083, CA268084, CA271273, CA274492, CA274494, CA274499, CA274502, CA274509, CA275808",,TRUE,,,,,list like Dataset Pubmed Id,"The PubMed identifer(s) associated with the development of the dataset. Multiple values permitted, comma separated.",,,TRUE,,,,,list like DatasetView_id,A unique primary key that enables record updates using schematic.,,,TRUE,,,,,unique From c085c678f1896ed045add9c3c52f1de8885d47d9 Mon Sep 17 00:00:00 2001 From: Orion Banks <49208907+Bankso@users.noreply.github.com> Date: Mon, 24 Jul 2023 13:13:44 -0700 Subject: [PATCH 03/15] Add 'EducationalResource_id' as attribute --- modules/education/annotationProperty.csv | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/modules/education/annotationProperty.csv b/modules/education/annotationProperty.csv index 1590bd9..79dd314 100644 --- a/modules/education/annotationProperty.csv +++ b/modules/education/annotationProperty.csv @@ -11,7 +11,7 @@ Resource Educational Level,"Educational context (pre-school, lower-primary, uppe Resource Description,Abstract or summary of the item.,,,TRUE,,,,OER,str Resource Origin Institution,Institution(s) of origin for this item. Multiple values should be provided as a comma separated list.,,,TRUE,,,,OER,list like Resource Language,Language of the item (not of the metadata). Multiple values should be provided as a comma separated list.,"aa, ab, ae, af, ak, am, an, ar, as, av, ay, az, ba, be, bg, bh, bi, bm, bn, bo, br, bs, ca, ca, ce, ch, co, cr, cs, cu, cv, cy, da, de, dv, dv, dz, ee, el, en, eo, es, et, eu, fa, ff, fi, fj, fo, fr, fy, ga, gd, gl, gn, gu, gv, ha, he, hi, ho, hr, ht, hu, hy, hz, ia, id, ie, ig, ii, ik, io, is, it, iu, ja, jv, ka, kg, ki, kj, kk, kl, km, kn, ko, kr, ks, ku, kv, kw, ky, la, lb, lg, li, ln, lo, lt, lu, lv, mg, mh, mi, mk, ml, mn, mr, ms, mt, my, na, nb, nd, ne, ng, nl, nn, no, nr, nv, ny, oc, oj, om, or, os, pa, pi, pl, ps, pt, qu, rm, rn, ro, ru, rw, sa, sc, sd, se, sg, si, sk, sl, sm, sn, so, sq, sr, ss, st, su, sv, sw, ta, te, tg, th, ti, tk, tl, tn, to, tr, ts, tt, tw, ty, ug, uk, ur, uz, ve, vi, vo, wa, wo, xh, yi, yo, za, zh, zu",,TRUE,,,,OER,list like :: regex fullmatch [a-z]{2} -Resource Contributors,The name(s) of the contributor(s) to the item. Multiple contributor names should be provided as a comma-separated list. ,,,TRUE,,,,OER,list like +Resource Contributors,The name(s) of the contributor(s) to the item. Multiple contributor names should be provided as a comma-separated list.,,,TRUE,,,,OER,list like Resource Grant Number,"The grant number(s) associated with the contributor(s) of the item. If no grant number listed is applicable, please select 'Affiliated/Non-Grant Associated'. Multiple values should be provided as a comma separated list.","Affiliated/Non-Grant Associated, CA184897, CA184898, CA188388, CA193313, CA193417, CA193419, CA193461, CA193489, CA195469, CA199315, CA202123, CA202144, CA202177, CA202229, CA202241, CA209891, CA209923, CA209971, CA209975, CA209978, CA209988, CA209992, CA209997, CA210152, CA210173, CA210180, CA210181, CA210184, CA210190, CA214282, CA214292, CA214297, CA214300, CA214354, CA214369, CA214381, CA214411, CA215709, CA215794, CA215798, CA215845, CA215848, CA217297, CA217376, CA217377, CA217378, CA217450, CA217456, CA217514, CA217613, CA217617, CA217655, CA220378, CA223976, CA224012, CA224013, CA224044, CA225088, CA225566, CA227136, CA227544, CA227550, CA228608, CA228963, CA231978, CA232137, CA232161, CA232209, CA232216, CA232382, CA232517, CA234787, CA235747, CA238475, CA238720, CA238728, CA240301, CA241137, CA241927, CA243004, CA243007, CA243072, CA243073, CA243075, CA244100, CA244101, CA244107, CA244109, CA245313, CA248890, CA249799, CA250040, CA250044, CA250046, CA250481, CA251443, CA253248, CA253472, CA253540, CA253547, CA253553, CA254200, CA254886, CA256054, CA256481, CA260432, CA261694, CA261701, CA261717, CA261719, CA261822, CA261841, CA261842, CA263001, CA264583, CA264610, CA264611, CA264620, CA267170, CA268069, CA268072, CA268083, CA268084, CA271273, CA274492, CA274494, CA274499, CA274502, CA274509, CA275808",,TRUE,,,,MC2/grant,list like Resource Secondary Topic,"Additional topics or keywords to describe the content of the item, in addition to the primary topic. Multiple values should be provided as a comma-separated list.",,,FALSE,,,,OER,list like Resource License,"The name of the license applied to the item by the contributor(s), if applicable. Multiple values should be provided as a comma separated list.","AAL, ADSL, AFL-1.1, AFL-1.2, AFL-2.0, AFL-2.1, AFL-3.0, AGPL-1.0, AGPL-3.0, AMDPLPA, AML, AMPAS, ANTLR-PD, APAFML, APL-1.0, APSL-1.0, APSL-1.1, APSL-1.2, APSL-2.0, Abstyles, Adobe-2006, Adobe-Glyph, Afmparse, Aladdin, Apache-1.0, Apache-1.1, Apache-2.0, Artistic-1.0, Artistic-1.0-Perl, Artistic-1.0-cl8, Artistic-2.0, BSD-2-Clause, BSD-2-Clause-FreeBSD, BSD-2-Clause-NetBSD, BSD-3-Clause, BSD-3-Clause-Attribution, BSD-3-Clause-Clear, BSD-3-Clause-LBNL, BSD-3-Clause-No-Nuclear-License, BSD-3-Clause-No-Nuclear-License-2014, BSD-3-Clause-No-Nuclear-Warranty, BSD-4-Clause, BSD-4-Clause-UC, BSD-Protection, BSD-Source-Code, BSD-style, BSL-1.0, Bahyph, Barr, Beerware, BitTorrent-1.0, BitTorrent-1.1, Borceux, CATOSL-1.1, CC-BY-1.0, CC-BY-2.0, CC-BY-2.5, CC-BY-3.0, CC-BY-4.0, CC-BY-NC-1.0, CC-BY-NC-2.0, CC-BY-NC-2.5, CC-BY-NC-3.0, CC-BY-NC-4.0, CC-BY-NC-ND-1.0, CC-BY-NC-ND-2.0, CC-BY-NC-ND-2.5, CC-BY-NC-ND-3.0, CC-BY-NC-ND-4.0, CC-BY-NC-SA-1.0, CC-BY-NC-SA-2.0, CC-BY-NC-SA-2.5, CC-BY-NC-SA-3.0, CC-BY-NC-SA-4.0, CC-BY-ND-1.0, CC-BY-ND-2.0, CC-BY-ND-2.5, CC-BY-ND-3.0, CC-BY-ND-4.0, CC-BY-SA-1.0, CC-BY-SA-2.0, CC-BY-SA-2.5, CC-BY-SA-3.0, CC-BY-SA-4.0, CC0-1.0, CDDL-1.0, CDDL-1.1, CECILL-1.0, CECILL-1.1, CECILL-2.0, CECILL-2.1, CECILL-B, CECILL-C, CNRI-Jython, CNRI-Python, CNRI-Python-GPL-Compatible, CPAL-1.0, CPL-1.0, CPOL-1.02, CUA-OPL-1.0, Caldera, ClArtistic, Condor-1.1, Crossword, CrystalStacker, Cube, D-FSL-1.0, DOC, DSDP, Dotseqn, ECL-1.0, ECL-2.0, EFL-1.0, EFL-2.0, EPL-1.0, EUDatagrid, EUPL-1.0, EUPL-1.1, Entessa, ErlPL-1.1, Eurosym, FSFAP, FSFUL, FSFULLR, FTL, Fair, Frameworx-1.0, FreeImage, Freeware, GFDL-1.1, GFDL-1.2, GFDL-1.3, GL2PS, GPL-1.0, GPL-2.0, GPL-3.0, Giftware, Glide, Glulxe, HPND, HaskellReport, IBM-pibs, ICU, IJG, IPA, IPL-1.0, ISC, ImageMagick, Imlib2, Info-ZIP, Intel, Intel-ACPI, Interbase-1.0, JSON, JasPer-2.0, LAL-1.2, LAL-1.3, LGPL-2.0, LGPL-2.1, LGPL-3.0, LGPLLR, LPL-1.0, LPL-1.02, LPPL-1.0, LPPL-1.1, LPPL-1.2, LPPL-1.3a, LPPL-1.3c, Latex2e, Leptonica, LiLiQ-P-1.1, LiLiQ-R-1.1, LiLiQ-Rplus-1.1, Libpng, MIT, MIT-CMU, MIT-advertising, MIT-enna, MIT-feh, MITNFA, MPL-1.0, MPL-1.1, MPL-2.0, MPL-2.0-no-copyleft-exception, MS-PL, MS-RL, MTLL, MakeIndex, MirOS, Motosoto, Multics, Mup, NASA-1.3, NBPL-1.0, NCSA, NGPL, NLOD-1.0, NLPL, NOSL, NPL-1.0, NPL-1.1, NPOSL-3.0, NRL, NTP, Naumen, NetCDF, Newsletr, Nokia, Not licensed, Noweb, Nunit, OCCT-PL, OCLC-2.0, ODbL-1.0, OFL-1.0, OFL-1.1, OGTSL, OLDAP-1.1, OLDAP-1.2, OLDAP-1.3, OLDAP-1.4, OLDAP-2.0, OLDAP-2.0.1, OLDAP-2.1, OLDAP-2.2, OLDAP-2.2.1, OLDAP-2.2.2, OLDAP-2.3, OLDAP-2.4, OLDAP-2.5, OLDAP-2.6, OLDAP-2.7, OLDAP-2.8, OML, OPL-1.0, OSET-PL-2.1, OSL-1.0, OSL-1.1, OSL-2.0, OSL-2.1, OSL-3.0, OpenSSL, Other, PDDL-1.0, PHP-3.0, PHP-3.01, Plexus, PostgreSQL, Proprietary, Python-2.0, QPL-1.0, Qhull, RHeCos-1.1, RPL-1.1, RPL-1.5, RPSL-1.0, RSA-MD, RSCPL, Rdisc, Ruby, SAX-PD, SCEA, SGI-B-1.0, SGI-B-1.1, SGI-B-2.0, SISSL, SISSL-1.2, SMLNJ, SMPPL, SNIA, SPL-1.0, SWL, Saxpath, Sendmail, SimPL-2.0, Sleepycat, Spencer-86, Spencer-94, Spencer-99, SugarCRM-1.1.3, TCL, TMate, TORQUE-1.1, TOSL, UPL-1.0, Unicode-TOU, Unlicense, VOSTROM, VSL-1.0, Vim, W3C, W3C-19980720, WTFPL, Watcom-1.0, Wsuipa, X11, XFree86-1.1, XSkat, Xerox, Xnet, YPL-1.0, YPL-1.1, ZPL-1.1, ZPL-2.0, ZPL-2.1, Zed, Zend-2.0, Zimbra-1.3, Zimbra-1.4, Zlib, bzip2-1.0.5, bzip2-1.0.6, curl, diffmark, dvipdfm, eGenix, gSOAP-1.3b, gnuplot, iMatix, libtiff, mpich2, psfrag, psutils, xinetd, xpp, zlib-acknowledgement",,FALSE,,,,OER,list like @@ -22,3 +22,4 @@ Resource Media Accessibility,"Accessibility features (Alternative Text, Audio De Resource Access Hazard,"Sensory hazards (Flashing, Motion, etc.) applicable to the item. Multiple values should be provided as a comma separated list.","Flashing, Motion, Simulation, Sound",,FALSE,,,,OER,list like Resource Dataset Alias,"URL or persistent identifier (DOI, Synapse ID) for any dataset(s) that is intended to be used with the item. Multiple values should be provided as a comma separated list.",,,FALSE,,,,MC2/dataset,list like Resource Tool Link,"URL or persistent identifier (DOI, Synapse ID) for any software or tool that is intended to be used with the item. Multiple values should be provided as a comma separated list.",,,FALSE,,,,MC2/tool,list like +EducationalResource_id,A unique primary key that enables record updates using schematic.,,,TRUE,,,,,unique From 21b4383733556d4e31c038445905d3453525afdb Mon Sep 17 00:00:00 2001 From: Orion Banks <49208907+Bankso@users.noreply.github.com> Date: Mon, 24 Jul 2023 13:14:51 -0700 Subject: [PATCH 04/15] Add 'EducationalResource_id' to 'EducationalResource' schema' --- modules/education/annotationProperty.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/education/annotationProperty.csv b/modules/education/annotationProperty.csv index 79dd314..5f4a57d 100644 --- a/modules/education/annotationProperty.csv +++ b/modules/education/annotationProperty.csv @@ -1,5 +1,5 @@ Attribute,Description,Valid Values,DependsOn,Required,Properties,Parent,DependsOn Component,Source,Validation Rules -Educational Resource,Manifest for describing educational resources.,,"Component, Resource Title, Resource Link, Resource Topic, Resource Activity Type, Resource Primary Format, Resource Intended Use, Resource Primary Audience, Resource Educational Level, Resource Description, Resource Origin Institution, Resource Language, Resource Contributors, Resource Grant Number, Resource Secondary Topic, Resource License, Resource Use Requirements, Resource Alias, Resource Internal Identifier, Resource Media Accessibility, Resource Access Hazard, Resource Dataset Alias, Resource Tool Link",FALSE,,,"Dataset, Tool, Grant",, +Educational Resource,Manifest for describing educational resources.,,"Component, EducationalResource_id, Resource Title, Resource Link, Resource Topic, Resource Activity Type, Resource Primary Format, Resource Intended Use, Resource Primary Audience, Resource Educational Level, Resource Description, Resource Origin Institution, Resource Language, Resource Contributors, Resource Grant Number, Resource Secondary Topic, Resource License, Resource Use Requirements, Resource Alias, Resource Internal Identifier, Resource Media Accessibility, Resource Access Hazard, Resource Dataset Alias, Resource Tool Link",FALSE,,,"Dataset, Tool, Grant",, Resource Title,Title of the item.,,,TRUE,,,,OER,str Resource Link,The URL or DOI that links to the item.,,,TRUE,,,,OER,url Resource Topic,"General topic or research context of the item. If 'other' is selected, please provide additional topics in the 'Resource Secondary Topic' field. Multiple values should be provided as a comma separated list.","Computational Model Development, Computational Resource, Diversity/Equity/Inclusion, Drug Resistance/Sensitivity, Epigenetics, Evolution, Experimental Model Development, Heterogeneity, Immunotherapy, Mechano-genetics, Mechano-resistance, Metabolism, Metastasis, Method/Assay Development, Microenvironment, Oncogenic Stress, Other, Outreach, Platform Development, Training Material, Tumor Progression, Tumor-Immune, Computer Science, Environmental Science, Information Science, Educational Technology, Anatomy/Physiology, Biology, Ecology, Genetics, Nutrition, Measurement and Data, Statistics and Probability, Chemistry, Physics, Systems Biology",,TRUE,,,,OER,list like From 72ec55352cf39c61d3013456ffd74a3783233a77 Mon Sep 17 00:00:00 2001 From: Orion Banks <49208907+Bankso@users.noreply.github.com> Date: Mon, 24 Jul 2023 13:16:48 -0700 Subject: [PATCH 05/15] Add 'GrantView_id' as attribute --- modules/grant/annotationProperty.csv | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/grant/annotationProperty.csv b/modules/grant/annotationProperty.csv index 0c26ecb..fcb8881 100644 --- a/modules/grant/annotationProperty.csv +++ b/modules/grant/annotationProperty.csv @@ -10,3 +10,4 @@ Grant Institution Name,The full name of the institution(s) associated with the g Grant Institution Alias,The alias of the institution(s) associated with the grant (e.g. UCSD). 1...*,"ASU, AU, BCM, BIDMC, BMC, BU, BWH, Barrow, CHOP, COH, CSHL, Caltech, Cleveland Clinic, Columbia, Cornell, DFCI, Dartmouth, Duke, Emory, GTech, HMS, HUJI, Harvard, Houston Methodist, ISB, IU, IUPUI, JHU, Jackson Laboratory, Lurie Children's Hospital, MGH, MIT, MSKCC, Mayo, Moffitt, NU, NYU, OHSU, PNNL, Pitt, Rockefeller University, SBU, Sage, Salk, StJude, Stanford, U Miami, UA, UAB, UCBerkeley, UCD, UCI, UCLA, UCMC, UCSD, UCSF, UChicago, UD, UFL, UIC, UMMS, UMichigan, UMinn, UNC, UNSW, UPenn, USC, UT Austin, UT Southwestern, UTHSCSA, UUtah, UVA, UW, UWM, University of Illinois, University of Texas MD Anderson Cancer Center, Vanderbilt, WCM, Wake Forest, Wistar, Yale",,TRUE,,,,,list like Grant Investigator,Investigator(s) associated witht the grant. 1...*,,,TRUE,,,,,list like Grant Consortium Name,Consortium(s) associated with the grant. 1...1,"CCBIR, CSBC, HTAN, ICBP, MetNet, NCI, NCI Clinical and Translational Exploratory/Developmental Studies, PDMC, PS-ON, Sage Bionetworks, TEC",,TRUE,,,,, +GrantView_id,A unique primary key that enables record updates using schematic.,,,TRUE,,,,,unique From 7101f4e2bf620c0dbdb01544c8239970b613f879 Mon Sep 17 00:00:00 2001 From: Orion Banks <49208907+Bankso@users.noreply.github.com> Date: Mon, 24 Jul 2023 13:17:56 -0700 Subject: [PATCH 06/15] Add 'GrantView_id' to 'GrantView' schema --- modules/grant/annotationProperty.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/grant/annotationProperty.csv b/modules/grant/annotationProperty.csv index fcb8881..858f40b 100644 --- a/modules/grant/annotationProperty.csv +++ b/modules/grant/annotationProperty.csv @@ -4,7 +4,7 @@ Grant Name,Name of the grant,,,TRUE,,,,, Grant Number,"Number of the grant (i.e. ""CA------"" format)",,,TRUE,,,,,regex search ^CA\d{6}$ Grant Abstract,Abstract for the grant,,,TRUE,,,,, Grant Type,Type of grant,"R01, R21, R37, U01, U24, U54",,TRUE,,,,, -Grant View,The denormalized manifest for grant submission.,,"Component, Grant Name, Grant Number, Grant Abstract, Grant Type, Grant Theme Name, Grant Institution Name, Grant Institution Alias, Grant Investigator, Grant Consortium Name",FALSE,,,"Theme, Institution, Consortium, Grant",, +Grant View,The denormalized manifest for grant submission.,,"Component, GrantView_id, Grant Name, Grant Number, Grant Abstract, Grant Type, Grant Theme Name, Grant Institution Name, Grant Institution Alias, Grant Investigator, Grant Consortium Name",FALSE,,,"Theme, Institution, Consortium, Grant",, Grant Theme Name,Theme(s) associated with the grant. 1...*,"Computational Model Development, Computational Resource, Drug Resistance/Sensitivity, Epigenetics, Evolution, Experimental Model Development, Heterogeneity, Immunotherapy, Mechano-genetics, Mechano-resistance, Metabolism, Metastasis, Method/Assay Development, Microenvironment, Oncogenic Stress, Platform Development, Tumor Progression, Tumor-Immune",,TRUE,,,,,list like Grant Institution Name,The full name of the institution(s) associated with the grant. (e.g. Harvard University). 1...*,"Arizona State University, Auburn University, Barrow Neurological Institute, Baylor College Of Medicine, Beth Israel Deaconess Hospital, Boston Medical Center, Boston University, Brigham and Womens Hospital, California Institute of Technology, Childrens Hospital of Philadelphia, City Of Hope, Cleveland Clinic, Cold Spring Harbor Laboratory, Columbia University, Cornell University, Dana-Farber Cancer Institute, Dartmouth College, Duke University, Emory University, Georgia Institute of Technology, Harvard Medical School, Harvard University, Hebrew University of Jerusalem, Houston Methodist, Indiana University, Indiana University - Purdue University Indianapolis, Institute for Systems Biology, Jackson Laboratory, Johns Hopkins University, Lurie Children's Hospital, Massachusetts General Hospital, Massachusetts Institute of Technology, Mayo Clinic, Memorial Sloan Kettering Cancer Center, Moffitt Cancer Center, New York University, Northwestern University, Oregon Health & Science University, Pacific Northwest National Laboratory, Rockefeller University, Sage Bionetworks, Salk Institute for Biological Studies, St. Jude Children's Research Hospital, Stanford University, Stony Brook University, The University of Texas Health Science Center at San Antonio, University of Alabama at Birmingham, University of Arizona, University of California; Berkeley, University of California; Irvine, University of California; Los Angeles, University of California; San Diego, University of California; San Francisco, University of Chicago, University of Chicago Medical Center, University of Colorado Denver, University of Delaware, University of Florida, University of Illinois, University of Illinois at Chicago, University of Massachusetts Medical School, University of Miami, University of Michigan, University of Minnesota, University of New South Wales, University of North Carolina at Chapel Hill, University of Pennsylvania, University of Pittsburgh, University of Southern California, University of Texas MD Anderson Cancer Center, University of Texas Southwestern Medical Center, University of Texas at Austin, University of Utah, University of Virginia, University of Washington, University of Wisconsin-Madison, Vanderbilt University, Wake Forest, Weill Cornell Medicine, Wistar Institute, Yale University",,TRUE,,,,,list like Grant Institution Alias,The alias of the institution(s) associated with the grant (e.g. UCSD). 1...*,"ASU, AU, BCM, BIDMC, BMC, BU, BWH, Barrow, CHOP, COH, CSHL, Caltech, Cleveland Clinic, Columbia, Cornell, DFCI, Dartmouth, Duke, Emory, GTech, HMS, HUJI, Harvard, Houston Methodist, ISB, IU, IUPUI, JHU, Jackson Laboratory, Lurie Children's Hospital, MGH, MIT, MSKCC, Mayo, Moffitt, NU, NYU, OHSU, PNNL, Pitt, Rockefeller University, SBU, Sage, Salk, StJude, Stanford, U Miami, UA, UAB, UCBerkeley, UCD, UCI, UCLA, UCMC, UCSD, UCSF, UChicago, UD, UFL, UIC, UMMS, UMichigan, UMinn, UNC, UNSW, UPenn, USC, UT Austin, UT Southwestern, UTHSCSA, UUtah, UVA, UW, UWM, University of Illinois, University of Texas MD Anderson Cancer Center, Vanderbilt, WCM, Wake Forest, Wistar, Yale",,TRUE,,,,,list like From 4b9b6bae7d3dc218de5eca274690c66223e101b8 Mon Sep 17 00:00:00 2001 From: Orion Banks <49208907+Bankso@users.noreply.github.com> Date: Mon, 24 Jul 2023 13:19:29 -0700 Subject: [PATCH 07/15] Add 'PersonView_id' as attribute --- modules/person/annotationProperty.csv | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/modules/person/annotationProperty.csv b/modules/person/annotationProperty.csv index b3aae5a..1184492 100644 --- a/modules/person/annotationProperty.csv +++ b/modules/person/annotationProperty.csv @@ -5,7 +5,7 @@ Alternative Names,"Other ways the individual's name is displayed. Multiple value Email,Email address of the individual,,,FALSE,,,,, Url,"URL, e.g., individual's home page address",,,FALSE,,,,, Orcid Id,Unique identifier (ORCID ID) of the individual,,,FALSE,,,,,regex search \d{4}\-\d{4}\-\d{4}\-\d{3}(\d|X) -Synapse Profile Id,Unique identifier (Synapse Profile ID) of the individual. See identifer in the url of the synapse profile page. ,,,FALSE,,,,,unique +Synapse Profile Id,"Unique identifier (Synapse Profile ID) of the individual. See identifer in the url of the synapse profile page. ",,,FALSE,,,,,unique Last Known Institution,Last known institutional affiliation of the individual.,,,TRUE,,,,, Working Group Participation,"CSBC/PSON working group(s) of which the individual is a member (current and former). Multiple values permitted, comma separated.","Cancer Metabolism, Cell and Tissue Mechanics, Education and Outreach, Image Analysis, Navigating Cancer with Science and Art, None, Patient Advocacy Working Group, Protein-Protein Interactions, Resource and Data Sharing",,TRUE,,,,,list like Chair Roles,"Committee or working group chair role(s) the individual fulfilled (current and former). Multiple values permitted, comma separated.","Annual Meeting, None, Steering Committee, Working Group",,TRUE,,,,,list like @@ -19,3 +19,4 @@ Person Publications,"A list of the pubmed Ids associated with the person. Multip Person Datasets,"A list of the dataset aliases (An alias of the dataset must be unique. Can be the GEO identifier such as GSE12345, or a DOI. No Greek Letters) associated with the person. Multiple values permitted, comma separated.",,,FALSE,,,,,list like Person Tools,"A list of the tool names associated with the person. Multiple values permitted, comma separated.",,,FALSE,,,,,list like Person Educational Resources,"A list of educational resource identifiers associated with the person. Multiple values permitted, comma separated.",,,FALSE,,,,,list like +PersonView_id,A unique primary key that enables record updates using schematic.,,,TRUE,,,,,unique From 7c36161bd1d57d8a4dd9801ad5722d503788b126 Mon Sep 17 00:00:00 2001 From: Orion Banks <49208907+Bankso@users.noreply.github.com> Date: Mon, 24 Jul 2023 13:20:33 -0700 Subject: [PATCH 08/15] Add 'PersonView_id' to 'PersonView' schema --- modules/person/annotationProperty.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/person/annotationProperty.csv b/modules/person/annotationProperty.csv index 1184492..dbb6b85 100644 --- a/modules/person/annotationProperty.csv +++ b/modules/person/annotationProperty.csv @@ -12,7 +12,7 @@ Chair Roles,"Committee or working group chair role(s) the individual fulfilled ( Consent For Portal Display,Consent from individual to display Person information in the CCKP,"No, Yes",,TRUE,,,,, Portal Display,Display content in CCKP,"FALSE, TRUE",,TRUE,,,,, Person Consortium,"Consortiums associated with a person, joined by uuids from the person and consortium table.",,"Component, Person, Consortium",FALSE,,,"Person, Consortium",, -Person View,The denormalized manifest for person submission.,,"Component, Person Grant Number, Person Consortium Name, Name, Alternative Names, Email, Url, Orcid Id, Synapse Profile Id, Last Known Institution, Working Group Participation, Chair Roles, Consent For Portal Display, Portal Display, Person Publications, Person Datasets, Person Tools, Person Educational Resources",FALSE,,,"Publication, Dataset, Tool, Consortium, Grant, Person, Educational Resource",, +Person View,The denormalized manifest for person submission.,,"Component, PersonView_id, Person Grant Number, Person Consortium Name, Name, Alternative Names, Email, Url, Orcid Id, Synapse Profile Id, Last Known Institution, Working Group Participation, Chair Roles, Consent For Portal Display, Portal Display, Person Publications, Person Datasets, Person Tools, Person Educational Resources",FALSE,,,"Publication, Dataset, Tool, Consortium, Grant, Person, Educational Resource",, Person Grant Number,"Grant number(s) associated with the person. Multiple values permitted, comma separated.","Affiliated/Non-Grant Associated, CA184897, CA184898, CA188388, CA193313, CA193417, CA193419, CA193461, CA193489, CA195469, CA199315, CA202123, CA202144, CA202177, CA202229, CA202241, CA209891, CA209923, CA209971, CA209975, CA209978, CA209988, CA209992, CA209997, CA210152, CA210173, CA210180, CA210181, CA210184, CA210190, CA214282, CA214292, CA214297, CA214300, CA214354, CA214369, CA214381, CA214411, CA215709, CA215794, CA215798, CA215845, CA215848, CA217297, CA217376, CA217377, CA217378, CA217450, CA217456, CA217514, CA217613, CA217617, CA217655, CA220378, CA223976, CA224012, CA224013, CA224044, CA225088, CA225566, CA227136, CA227544, CA227550, CA228608, CA228963, CA231978, CA232137, CA232161, CA232209, CA232216, CA232382, CA232517, CA234787, CA235747, CA238475, CA238720, CA238728, CA240301, CA241137, CA241927, CA243004, CA243007, CA243072, CA243073, CA243075, CA244100, CA244101, CA244107, CA244109, CA245313, CA248890, CA249799, CA250040, CA250044, CA250046, CA250481, CA251443, CA253248, CA253472, CA253540, CA253547, CA253553, CA254200, CA254886, CA256054, CA256481, CA260432, CA261694, CA261701, CA261717, CA261719, CA261822, CA261841, CA261842, CA263001, CA264583, CA264610, CA264611, CA264620, CA267170, CA268069, CA268072, CA268083, CA268084, CA271273, CA274492, CA274494, CA274499, CA274502, CA274509, CA275808",,TRUE,,,,,list like Person Consortium Name,"Consortium(s) associated with the person. Multiple values permitted, comma separated.","CCBIR, CSBC, HTAN, ICBP, MetNet, NCI, NCI Clinical and Translational Exploratory/Developmental Studies, PDMC, PS-ON, Sage Bionetworks, TEC",,TRUE,,,,,list like Person Publications,"A list of the pubmed Ids associated with the person. Multiple values permitted, comma separated.",,,FALSE,,,,,list like From bbf143aff94a11ac9a40f0aa2629d53511ba9aad Mon Sep 17 00:00:00 2001 From: Orion Banks <49208907+Bankso@users.noreply.github.com> Date: Mon, 24 Jul 2023 13:23:30 -0700 Subject: [PATCH 09/15] Add 'ProjectView_id' as attribute --- modules/project/annotationProperty.csv | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/modules/project/annotationProperty.csv b/modules/project/annotationProperty.csv index 32c77e8..c872aee 100644 --- a/modules/project/annotationProperty.csv +++ b/modules/project/annotationProperty.csv @@ -6,5 +6,6 @@ Project Description,Description of the project,,,TRUE,,,,, Project Investigator,Investigator(s) associated witht the project. 1...*,,,TRUE,,,,,list like Project View,The denormalized manifest for project submission.,,"Component, Project Name, Project Type, Project Description, Project Investigator, Project Consortium Name, Project Grant Number",FALSE,,,"Project, Grant",, Project Grant Number,Grant number(s) associated with the project 1...*,"Affiliated/Non-Grant Associated, CA184897, CA184898, CA188388, CA193313, CA193417, CA193419, CA193461, CA193489, CA195469, CA199315, CA202123, CA202144, CA202177, CA202229, CA202241, CA209891, CA209923, CA209971, CA209975, CA209978, CA209988, CA209992, CA209997, CA210152, CA210173, CA210180, CA210181, CA210184, CA210190, CA214282, CA214292, CA214297, CA214300, CA214354, CA214369, CA214381, CA214411, CA215709, CA215794, CA215798, CA215845, CA215848, CA217297, CA217376, CA217377, CA217378, CA217450, CA217456, CA217514, CA217613, CA217617, CA217655, CA220378, CA223976, CA224012, CA224013, CA224044, CA225088, CA225566, CA227136, CA227544, CA227550, CA228608, CA228963, CA231978, CA232137, CA232161, CA232209, CA232216, CA232382, CA232517, CA234787, CA235747, CA238475, CA238720, CA238728, CA240301, CA241137, CA241927, CA243004, CA243007, CA243072, CA243073, CA243075, CA244100, CA244101, CA244107, CA244109, CA245313, CA248890, CA249799, CA250040, CA250044, CA250046, CA250481, CA251443, CA253248, CA253472, CA253540, CA253547, CA253553, CA254200, CA254886, CA256054, CA256481, CA260432, CA261694, CA261701, CA261717, CA261719, CA261822, CA261841, CA261842, CA263001, CA264583, CA264610, CA264611, CA264620, CA267170, CA268069, CA268072, CA268083, CA268084, CA271273, CA274492, CA274494, CA274499, CA274502, CA274509, CA275808",,TRUE,,,,,list like -Project Consorium Name, Consortium(s) associated with the project. 1...1,,,TRUE,,,,, -Project Consortium Name,,"CCBIR, CSBC, HTAN, ICBP, MetNet, NCI, NCI Clinical and Translational Exploratory/Developmental Studies, PDMC, PS-ON, Sage Bionetworks, TEC",,,,,,, +Project Consorium Name," Consortium(s) associated with the project. 1...1",,,TRUE,,,,, +Project Consortium Name,,"CCBIR, CSBC, HTAN, ICBP, MetNet, NCI, NCI Clinical and Translational Exploratory/Developmental Studies, PDMC, PS-ON, Sage Bionetworks, TEC",,TRUE,,,,, +ProjectView_id,A unique primary key that enables record updates using schematic.,,,TRUE,,,,,unique From 1238ffafb8e87e46d630dab10060debb5b6fc7f9 Mon Sep 17 00:00:00 2001 From: Orion Banks <49208907+Bankso@users.noreply.github.com> Date: Mon, 24 Jul 2023 13:24:25 -0700 Subject: [PATCH 10/15] Add 'ProjectView_id' to 'ProjectView' schema --- modules/project/annotationProperty.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/project/annotationProperty.csv b/modules/project/annotationProperty.csv index c872aee..13b0a34 100644 --- a/modules/project/annotationProperty.csv +++ b/modules/project/annotationProperty.csv @@ -4,7 +4,7 @@ Project Name,Name of the project,,,TRUE,,,,, Project Type,Type of project,"Core, Project",,TRUE,,,,, Project Description,Description of the project,,,TRUE,,,,, Project Investigator,Investigator(s) associated witht the project. 1...*,,,TRUE,,,,,list like -Project View,The denormalized manifest for project submission.,,"Component, Project Name, Project Type, Project Description, Project Investigator, Project Consortium Name, Project Grant Number",FALSE,,,"Project, Grant",, +Project View,The denormalized manifest for project submission.,,"Component, ProjectView_id, Project Name, Project Type, Project Description, Project Investigator, Project Consortium Name, Project Grant Number",FALSE,,,"Project, Grant",, Project Grant Number,Grant number(s) associated with the project 1...*,"Affiliated/Non-Grant Associated, CA184897, CA184898, CA188388, CA193313, CA193417, CA193419, CA193461, CA193489, CA195469, CA199315, CA202123, CA202144, CA202177, CA202229, CA202241, CA209891, CA209923, CA209971, CA209975, CA209978, CA209988, CA209992, CA209997, CA210152, CA210173, CA210180, CA210181, CA210184, CA210190, CA214282, CA214292, CA214297, CA214300, CA214354, CA214369, CA214381, CA214411, CA215709, CA215794, CA215798, CA215845, CA215848, CA217297, CA217376, CA217377, CA217378, CA217450, CA217456, CA217514, CA217613, CA217617, CA217655, CA220378, CA223976, CA224012, CA224013, CA224044, CA225088, CA225566, CA227136, CA227544, CA227550, CA228608, CA228963, CA231978, CA232137, CA232161, CA232209, CA232216, CA232382, CA232517, CA234787, CA235747, CA238475, CA238720, CA238728, CA240301, CA241137, CA241927, CA243004, CA243007, CA243072, CA243073, CA243075, CA244100, CA244101, CA244107, CA244109, CA245313, CA248890, CA249799, CA250040, CA250044, CA250046, CA250481, CA251443, CA253248, CA253472, CA253540, CA253547, CA253553, CA254200, CA254886, CA256054, CA256481, CA260432, CA261694, CA261701, CA261717, CA261719, CA261822, CA261841, CA261842, CA263001, CA264583, CA264610, CA264611, CA264620, CA267170, CA268069, CA268072, CA268083, CA268084, CA271273, CA274492, CA274494, CA274499, CA274502, CA274509, CA275808",,TRUE,,,,,list like Project Consorium Name," Consortium(s) associated with the project. 1...1",,,TRUE,,,,, Project Consortium Name,,"CCBIR, CSBC, HTAN, ICBP, MetNet, NCI, NCI Clinical and Translational Exploratory/Developmental Studies, PDMC, PS-ON, Sage Bionetworks, TEC",,TRUE,,,,, From 0b8f0e0d35d46271015c6c8ab9b497160762dbc7 Mon Sep 17 00:00:00 2001 From: Orion Banks <49208907+Bankso@users.noreply.github.com> Date: Mon, 24 Jul 2023 13:25:54 -0700 Subject: [PATCH 11/15] Add 'PublicationView_id' as attribute --- modules/publication/annotationProperty.csv | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/publication/annotationProperty.csv b/modules/publication/annotationProperty.csv index e2bdf6a..8896a5a 100644 --- a/modules/publication/annotationProperty.csv +++ b/modules/publication/annotationProperty.csv @@ -19,3 +19,4 @@ Publication Grant Number,"Relevant grant number associated witht the publication Publication Dataset Alias,"A list of the dataset aliases (An alias of the dataset must be unique. Can be the GEO identifier such as GSE12345, or a DOI. No Greek Letters) associated with the publication. Multiple values permitted, comma separated.",,,FALSE,,,,,list like Publication View DCA,The denormalized manifest for publication submission with component_id field for DCA upsert function.,,"Component, PublicationViewDCA_id, Publication Grant Number, Publication Doi, Publication Journal, Pubmed Id, Pubmed Url, Publication Title, Publication Year, Publication Keywords, Publication Authors, Publication Abstract, Publication Assay, Publication Tumor Type, Publication Tissue, Publication Accessibility, Publication Dataset Alias",FALSE,,,"Dataset, Tool, Grant, Publication",, PublicationViewDCA_id,Unique identifier that allows schematic to update and insert entries.,,,TRUE,,,,,unique +PublicationView_id,A unique primary key that enables record updates using schematic.,,,TRUE,,,,,unique From 83adc3914720d8867d5bb0741976183af04685f5 Mon Sep 17 00:00:00 2001 From: Orion Banks <49208907+Bankso@users.noreply.github.com> Date: Mon, 24 Jul 2023 13:27:08 -0700 Subject: [PATCH 12/15] Add 'PublicationView_id' to 'PublicationView' schema --- modules/publication/annotationProperty.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/publication/annotationProperty.csv b/modules/publication/annotationProperty.csv index 8896a5a..d4bd035 100644 --- a/modules/publication/annotationProperty.csv +++ b/modules/publication/annotationProperty.csv @@ -14,7 +14,7 @@ Publication Tumor Type,"Tumor type(s) associated with the publication. Multiple Publication Tissue,"Tissue type(s) associated with the publication. Multiple values permitted, comma separated.","Gonad, Abdominal Esophagus, Adipose Tissue, Adrenal Gland, Alveolus, Aorta, Artery, Ascending Colon, Bile Duct, Bladder, Blood, Blood Vessel, Bone, Bone Marrow, Brain, Breast, Caecum, Cancer-Associated Fibroblast, Cardia, Cartilage, Cervix Uteri, Choroid, Colon, Connective and Soft Tissue, Cornea, Duodenum, Ear, Embryo, Embryonic Heart, Endocervix, Endometrium, Endothelium, Epithelium, Esophagus, Eye, Fallopian Tube, Foreskin, Frontal Lobe, Gastroesophageal Junction, Gastrointestinal Tract, Genitourinary, Hair Follicle, Head and Neck, Heart, Heart Muscle, Hematopoietic System, Hippocampus, Intestine, Intra-Abdominal Lymph Nodes, Intrathoracic Lymph Nodes, Joint, Kidney, Larynx, Ligament, Liver, Lung, Lymph, Lymph Node, Lymph Nodes of Axilla or Arm, Lymph Nodes of Inguinal Region or Leg, Lymphatic System, Lymphoid Tissue, Main Bronchus, Mammary Gland, Meninges, Mesenchyme, Mucosa, Muscle, Nasal Cavity, Nervous System, Not Applicable, Olfactory Mucosa, Omentum, Oral Cavity, Oral Mucosa, Ovary, Pancreas, Pelvic Lymph Nodes, Pending Annotation, Periodontal Ligament, Peripheral Nerves, Peritoneum, Pharynx, Pituitary Gland, Placenta, Pleura, Prostate Gland, Rectum, Reproductive System, Respiratory System, Salivary Gland, Sclera, Sinonasal Tract, Skin, Small Intestine, Spinal Cord, Spleen, Stomach, Synovial Membrane, Tendon, Testis, Thymus, Thyroid Gland, Tongue, Tonsil, Trachea, Umbilical Cord, Unspecified, Uterus, Vagina, Vascular Endothelium, Vein, Vertebra, Peripheral Blood Mononuclear Cell",,TRUE,,,,,list like Publication Accessibility,Whether there are non-monetary restrictions on accessing an the publication.,"Open Access, Restricted Access",,TRUE,,,,, Publication Grant,"Publications associated with a grant, joined by uuids from the publication and grant table. ",,"Component, Publication, Grant",FALSE,,,"Publication, Grant",, -Publication View,The denormalized manifest for publication submission.,,"Component, Publication Grant Number, Publication Doi, Publication Journal, Pubmed Id, Pubmed Url, Publication Title, Publication Year, Publication Keywords, Publication Authors, Publication Abstract, Publication Assay, Publication Tumor Type, Publication Tissue, Publication Accessibility, Publication Dataset Alias",FALSE,,,"Dataset, Tool, Grant, Publication",, +Publication View,The denormalized manifest for publication submission.,,"Component, PublicationView_id, Publication Grant Number, Publication Doi, Publication Journal, Pubmed Id, Pubmed Url, Publication Title, Publication Year, Publication Keywords, Publication Authors, Publication Abstract, Publication Assay, Publication Tumor Type, Publication Tissue, Publication Accessibility, Publication Dataset Alias",FALSE,,,"Dataset, Tool, Grant, Publication",, Publication Grant Number,"Relevant grant number associated witht the publication's development. Multiple values permitted, comma separated.","Affiliated/Non-Grant Associated, CA184897, CA184898, CA188388, CA193313, CA193417, CA193419, CA193461, CA193489, CA195469, CA199315, CA202123, CA202144, CA202177, CA202229, CA202241, CA209891, CA209923, CA209971, CA209975, CA209978, CA209988, CA209992, CA209997, CA210152, CA210173, CA210180, CA210181, CA210184, CA210190, CA214282, CA214292, CA214297, CA214300, CA214354, CA214369, CA214381, CA214411, CA215709, CA215794, CA215798, CA215845, CA215848, CA217297, CA217376, CA217377, CA217378, CA217450, CA217456, CA217514, CA217613, CA217617, CA217655, CA220378, CA223976, CA224012, CA224013, CA224044, CA225088, CA225566, CA227136, CA227544, CA227550, CA228608, CA228963, CA231978, CA232137, CA232161, CA232209, CA232216, CA232382, CA232517, CA234787, CA235747, CA238475, CA238720, CA238728, CA240301, CA241137, CA241927, CA243004, CA243007, CA243072, CA243073, CA243075, CA244100, CA244101, CA244107, CA244109, CA245313, CA248890, CA249799, CA250040, CA250044, CA250046, CA250481, CA251443, CA253248, CA253472, CA253540, CA253547, CA253553, CA254200, CA254886, CA256054, CA256481, CA260432, CA261694, CA261701, CA261717, CA261719, CA261822, CA261841, CA261842, CA263001, CA264583, CA264610, CA264611, CA264620, CA267170, CA268069, CA268072, CA268083, CA268084, CA271273, CA274492, CA274494, CA274499, CA274502, CA274509, CA275808",,TRUE,,,,,list like Publication Dataset Alias,"A list of the dataset aliases (An alias of the dataset must be unique. Can be the GEO identifier such as GSE12345, or a DOI. No Greek Letters) associated with the publication. Multiple values permitted, comma separated.",,,FALSE,,,,,list like Publication View DCA,The denormalized manifest for publication submission with component_id field for DCA upsert function.,,"Component, PublicationViewDCA_id, Publication Grant Number, Publication Doi, Publication Journal, Pubmed Id, Pubmed Url, Publication Title, Publication Year, Publication Keywords, Publication Authors, Publication Abstract, Publication Assay, Publication Tumor Type, Publication Tissue, Publication Accessibility, Publication Dataset Alias",FALSE,,,"Dataset, Tool, Grant, Publication",, From f75cbe13562d1951ab274b7f2bdf12cdbf54da35 Mon Sep 17 00:00:00 2001 From: Orion Banks <49208907+Bankso@users.noreply.github.com> Date: Mon, 24 Jul 2023 13:28:48 -0700 Subject: [PATCH 13/15] Add 'ToolView_id' as attribute --- modules/tool/annotationProperty.csv | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/tool/annotationProperty.csv b/modules/tool/annotationProperty.csv index c0f61fe..eae0dab 100644 --- a/modules/tool/annotationProperty.csv +++ b/modules/tool/annotationProperty.csv @@ -32,3 +32,4 @@ Tool Grant,"Tools associated with a grant, joined by uuids from the tool table a Tool View,The denormalized manifest for tool submission.,,"Component, Tool Pubmed Id, Tool Grant Number, Tool Name, Tool Description, Tool Homepage, Tool Version, Tool Operation, Tool Input Data, Tool Output Data, Tool Input Format, Tool Output Format, Tool Function Note, Tool Cmd, Tool Type, Tool Topic, Tool Operating System, Tool Language, Tool License, Tool Cost, Tool Accessibility, Tool Download Url, Tool Download Type, Tool Download Note, Tool Download Version, Tool Documentation Url, Tool Documentation Type, Tool Documentation Note, Tool Link Url, Tool Link Type, Tool Link Note",FALSE,,,"Publication, Dataset, Grant, Tool",, Tool Grant Number,"Grant number associated with the tool's development. Multiple values permitted, comma separated.","Affiliated/Non-Grant Associated, CA184897, CA184898, CA188388, CA193313, CA193417, CA193419, CA193461, CA193489, CA195469, CA199315, CA202123, CA202144, CA202177, CA202229, CA202241, CA209891, CA209923, CA209971, CA209975, CA209978, CA209988, CA209992, CA209997, CA210152, CA210173, CA210180, CA210181, CA210184, CA210190, CA214282, CA214292, CA214297, CA214300, CA214354, CA214369, CA214381, CA214411, CA215709, CA215794, CA215798, CA215845, CA215848, CA217297, CA217376, CA217377, CA217378, CA217450, CA217456, CA217514, CA217613, CA217617, CA217655, CA220378, CA223976, CA224012, CA224013, CA224044, CA225088, CA225566, CA227136, CA227544, CA227550, CA228608, CA228963, CA231978, CA232137, CA232161, CA232209, CA232216, CA232382, CA232517, CA234787, CA235747, CA238475, CA238720, CA238728, CA240301, CA241137, CA241927, CA243004, CA243007, CA243072, CA243073, CA243075, CA244100, CA244101, CA244107, CA244109, CA245313, CA248890, CA249799, CA250040, CA250044, CA250046, CA250481, CA251443, CA253248, CA253472, CA253540, CA253547, CA253553, CA254200, CA254886, CA256054, CA256481, CA260432, CA261694, CA261701, CA261717, CA261719, CA261822, CA261841, CA261842, CA263001, CA264583, CA264610, CA264611, CA264620, CA267170, CA268069, CA268072, CA268083, CA268084, CA271273, CA274492, CA274494, CA274499, CA274502, CA274509, CA275808",,TRUE,,,,,list like Tool Pubmed Id,The pubMed identifer associated with the development of the tool.,,,FALSE,,,,,int +ToolView_id,A unique primary key that enables record updates using schematic.,,,TRUE,,,,,unique From 4dc5430f2ead08737ee5549b06341f9bf3b0dbc3 Mon Sep 17 00:00:00 2001 From: Orion Banks <49208907+Bankso@users.noreply.github.com> Date: Mon, 24 Jul 2023 13:29:59 -0700 Subject: [PATCH 14/15] Add 'ToolView_id' to 'ToolView' schema --- modules/tool/annotationProperty.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/tool/annotationProperty.csv b/modules/tool/annotationProperty.csv index eae0dab..fe710cb 100644 --- a/modules/tool/annotationProperty.csv +++ b/modules/tool/annotationProperty.csv @@ -29,7 +29,7 @@ Tool Link Url,A link of some relevance to the software (URL).,,,FALSE,,,,biotool Tool Link Type,"The type of data, information or system that is obtained when the link is resolved. Multiple values permitted, comma separated.","Discussion Forum, Galaxy Service, Helpdesk, Issue Tracker, Mailing list, Mirror, Other, Repository, Service, Social Media, Software Catalogue, Technical Monitoring",,FALSE,,,,biotoolsschema,list like Tool Link Note,Comment about the link.,,,FALSE,,,,biotoolsschema, Tool Grant,"Tools associated with a grant, joined by uuids from the tool table and grant table.",,"Component, Tool, Grant",FALSE,,,"Tool, Grant",, -Tool View,The denormalized manifest for tool submission.,,"Component, Tool Pubmed Id, Tool Grant Number, Tool Name, Tool Description, Tool Homepage, Tool Version, Tool Operation, Tool Input Data, Tool Output Data, Tool Input Format, Tool Output Format, Tool Function Note, Tool Cmd, Tool Type, Tool Topic, Tool Operating System, Tool Language, Tool License, Tool Cost, Tool Accessibility, Tool Download Url, Tool Download Type, Tool Download Note, Tool Download Version, Tool Documentation Url, Tool Documentation Type, Tool Documentation Note, Tool Link Url, Tool Link Type, Tool Link Note",FALSE,,,"Publication, Dataset, Grant, Tool",, +Tool View,The denormalized manifest for tool submission.,,"Component, ToolView_id, Tool Pubmed Id, Tool Grant Number, Tool Name, Tool Description, Tool Homepage, Tool Version, Tool Operation, Tool Input Data, Tool Output Data, Tool Input Format, Tool Output Format, Tool Function Note, Tool Cmd, Tool Type, Tool Topic, Tool Operating System, Tool Language, Tool License, Tool Cost, Tool Accessibility, Tool Download Url, Tool Download Type, Tool Download Note, Tool Download Version, Tool Documentation Url, Tool Documentation Type, Tool Documentation Note, Tool Link Url, Tool Link Type, Tool Link Note",FALSE,,,"Publication, Dataset, Grant, Tool",, Tool Grant Number,"Grant number associated with the tool's development. Multiple values permitted, comma separated.","Affiliated/Non-Grant Associated, CA184897, CA184898, CA188388, CA193313, CA193417, CA193419, CA193461, CA193489, CA195469, CA199315, CA202123, CA202144, CA202177, CA202229, CA202241, CA209891, CA209923, CA209971, CA209975, CA209978, CA209988, CA209992, CA209997, CA210152, CA210173, CA210180, CA210181, CA210184, CA210190, CA214282, CA214292, CA214297, CA214300, CA214354, CA214369, CA214381, CA214411, CA215709, CA215794, CA215798, CA215845, CA215848, CA217297, CA217376, CA217377, CA217378, CA217450, CA217456, CA217514, CA217613, CA217617, CA217655, CA220378, CA223976, CA224012, CA224013, CA224044, CA225088, CA225566, CA227136, CA227544, CA227550, CA228608, CA228963, CA231978, CA232137, CA232161, CA232209, CA232216, CA232382, CA232517, CA234787, CA235747, CA238475, CA238720, CA238728, CA240301, CA241137, CA241927, CA243004, CA243007, CA243072, CA243073, CA243075, CA244100, CA244101, CA244107, CA244109, CA245313, CA248890, CA249799, CA250040, CA250044, CA250046, CA250481, CA251443, CA253248, CA253472, CA253540, CA253547, CA253553, CA254200, CA254886, CA256054, CA256481, CA260432, CA261694, CA261701, CA261717, CA261719, CA261822, CA261841, CA261842, CA263001, CA264583, CA264610, CA264611, CA264620, CA267170, CA268069, CA268072, CA268083, CA268084, CA271273, CA274492, CA274494, CA274499, CA274502, CA274509, CA275808",,TRUE,,,,,list like Tool Pubmed Id,The pubMed identifer associated with the development of the tool.,,,FALSE,,,,,int ToolView_id,A unique primary key that enables record updates using schematic.,,,TRUE,,,,,unique From 7e404786d8a0895f4e193bc2f2a33111f0629ee8 Mon Sep 17 00:00:00 2001 From: "mc2center-bot[bot]" Date: Mon, 24 Jul 2023 20:45:49 +0000 Subject: [PATCH 15/15] build jsonld --- mc2.model.csv | 25 ++-- mc2.model.jsonld | 158 ++++++++++++++++++++++++- modules/person/annotationProperty.csv | 2 +- modules/project/annotationProperty.csv | 2 +- 4 files changed, 174 insertions(+), 13 deletions(-) diff --git a/mc2.model.csv b/mc2.model.csv index ab674bc..e8c66fa 100644 --- a/mc2.model.csv +++ b/mc2.model.csv @@ -19,10 +19,11 @@ Dataset Tumor Type,"The tumor type(s), if applicable, of the data collected on. Dataset Tissue,"Tissue type(s) associated with the dataset. Multiple values permitted, comma separated.","Gonad, Abdominal Esophagus, Adipose Tissue, Adrenal Gland, Alveolus, Aorta, Artery, Ascending Colon, Bile Duct, Bladder, Blood, Blood Vessel, Bone, Bone Marrow, Brain, Breast, Caecum, Cancer-Associated Fibroblast, Cardia, Cartilage, Cervix Uteri, Choroid, Colon, Connective and Soft Tissue, Cornea, Duodenum, Ear, Embryo, Embryonic Heart, Endocervix, Endometrium, Endothelium, Epithelium, Esophagus, Eye, Fallopian Tube, Foreskin, Frontal Lobe, Gastroesophageal Junction, Gastrointestinal Tract, Genitourinary, Hair Follicle, Head and Neck, Heart, Heart Muscle, Hematopoietic System, Hippocampus, Intestine, Intra-Abdominal Lymph Nodes, Intrathoracic Lymph Nodes, Joint, Kidney, Larynx, Ligament, Liver, Lung, Lymph, Lymph Node, Lymph Nodes of Axilla or Arm, Lymph Nodes of Inguinal Region or Leg, Lymphatic System, Lymphoid Tissue, Main Bronchus, Mammary Gland, Meninges, Mesenchyme, Mucosa, Muscle, Nasal Cavity, Nervous System, Not Applicable, Olfactory Mucosa, Omentum, Oral Cavity, Oral Mucosa, Ovary, Pancreas, Pelvic Lymph Nodes, Pending Annotation, Periodontal Ligament, Peripheral Nerves, Peritoneum, Pharynx, Pituitary Gland, Placenta, Pleura, Prostate Gland, Rectum, Reproductive System, Respiratory System, Salivary Gland, Sclera, Sinonasal Tract, Skin, Small Intestine, Spinal Cord, Spleen, Stomach, Synovial Membrane, Tendon, Testis, Thymus, Thyroid Gland, Tongue, Tonsil, Trachea, Umbilical Cord, Unspecified, Uterus, Vagina, Vascular Endothelium, Vein, Vertebra, Peripheral Blood Mononuclear Cell",,TRUE,,,,,list like Dataset File Formats,"A list of file formats associated with the dataset. Multiple values permitted, comma separated.","AVI, BAI, BAM, BED, CDS, CHP, COOL, CSV, DB, DS_Store, FASTA, FASTQ, FCS, FIG, FREQ, GCG, GCT, GCTx, GFF3, GTF, GZIP Format, HDF, HDF5, HTML, IDAT, JPG, JSON, LIF, MAP, MAT, MATLAB script, MSF, MTX, PDF, PNG, PZFX, Python Script, R File Format, RAW, RDS, ROUT, RPROJ, RTF, SGI, SRA, STAT, TAR Format, TDF, TIFF, TSV, TXT, VCF, WIG, XML, ZIP, bed12, bedgraph, cel, cloupe, docx, mzIdentML, mzXML, pptx, rcc, xls, xlsx, MGF, BIGWIG, H5AD, H5, SF, PKL, BPM, Unspecified, Pending Annotation",,FALSE,,,,,list like Dataset Grant,"Datasets associated with a grant, joined by uuids from the dataset and grant table.",,"Component. Dataset, Grant",FALSE,,,"Dataset, Grant",, -Dataset View,The denormalized manifest for dataset submission.,,"Component, Dataset Pubmed Id, Dataset Grant Number, Dataset Name, Dataset Alias, Dataset Description, Dataset Design, Dataset Assay, Dataset Species, Dataset Tumor Type, Dataset Tissue, Dataset Url, Dataset File Formats",FALSE,,,"Publication, Grant, Dataset",, +Dataset View,The denormalized manifest for dataset submission.,,"Component, DatasetView_id, Dataset Pubmed Id, Dataset Grant Number, Dataset Name, Dataset Alias, Dataset Description, Dataset Design, Dataset Assay, Dataset Species, Dataset Tumor Type, Dataset Tissue, Dataset Url, Dataset File Formats",FALSE,,,"Publication, Grant, Dataset",, Dataset Grant Number,"Grant number(s) associated with the dataset's development. Multiple values permitted, comma separated.","Affiliated/Non-Grant Associated, CA184897, CA184898, CA188388, CA193313, CA193417, CA193419, CA193461, CA193489, CA195469, CA199315, CA202123, CA202144, CA202177, CA202229, CA202241, CA209891, CA209923, CA209971, CA209975, CA209978, CA209988, CA209992, CA209997, CA210152, CA210173, CA210180, CA210181, CA210184, CA210190, CA214282, CA214292, CA214297, CA214300, CA214354, CA214369, CA214381, CA214411, CA215709, CA215794, CA215798, CA215845, CA215848, CA217297, CA217376, CA217377, CA217378, CA217450, CA217456, CA217514, CA217613, CA217617, CA217655, CA220378, CA223976, CA224012, CA224013, CA224044, CA225088, CA225566, CA227136, CA227544, CA227550, CA228608, CA228963, CA231978, CA232137, CA232161, CA232209, CA232216, CA232382, CA232517, CA234787, CA235747, CA238475, CA238720, CA238728, CA240301, CA241137, CA241927, CA243004, CA243007, CA243072, CA243073, CA243075, CA244100, CA244101, CA244107, CA244109, CA245313, CA248890, CA249799, CA250040, CA250044, CA250046, CA250481, CA251443, CA253248, CA253472, CA253540, CA253547, CA253553, CA254200, CA254886, CA256054, CA256481, CA260432, CA261694, CA261701, CA261717, CA261719, CA261822, CA261841, CA261842, CA263001, CA264583, CA264610, CA264611, CA264620, CA267170, CA268069, CA268072, CA268083, CA268084, CA271273, CA274492, CA274494, CA274499, CA274502, CA274509, CA275808",,TRUE,,,,,list like Dataset Pubmed Id,"The PubMed identifer(s) associated with the development of the dataset. Multiple values permitted, comma separated.",,,TRUE,,,,,list like -Educational Resource,Manifest for describing educational resources.,,"Component, Resource Title, Resource Link, Resource Topic, Resource Activity Type, Resource Primary Format, Resource Intended Use, Resource Primary Audience, Resource Educational Level, Resource Description, Resource Origin Institution, Resource Language, Resource Contributors, Resource Grant Number, Resource Secondary Topic, Resource License, Resource Use Requirements, Resource Alias, Resource Internal Identifier, Resource Media Accessibility, Resource Access Hazard, Resource Dataset Alias, Resource Tool Link",FALSE,,,"Dataset, Tool, Grant",, +DatasetView_id,A unique primary key that enables record updates using schematic.,,,TRUE,,,,,unique +Educational Resource,Manifest for describing educational resources.,,"Component, EducationalResource_id, Resource Title, Resource Link, Resource Topic, Resource Activity Type, Resource Primary Format, Resource Intended Use, Resource Primary Audience, Resource Educational Level, Resource Description, Resource Origin Institution, Resource Language, Resource Contributors, Resource Grant Number, Resource Secondary Topic, Resource License, Resource Use Requirements, Resource Alias, Resource Internal Identifier, Resource Media Accessibility, Resource Access Hazard, Resource Dataset Alias, Resource Tool Link",FALSE,,,"Dataset, Tool, Grant",, Resource Title,Title of the item.,,,TRUE,,,,OER,str Resource Link,The URL or DOI that links to the item.,,,TRUE,,,,OER,url Resource Topic,"General topic or research context of the item. If 'other' is selected, please provide additional topics in the 'Resource Secondary Topic' field. Multiple values should be provided as a comma separated list.","Computational Model Development, Computational Resource, Diversity/Equity/Inclusion, Drug Resistance/Sensitivity, Epigenetics, Evolution, Experimental Model Development, Heterogeneity, Immunotherapy, Mechano-genetics, Mechano-resistance, Metabolism, Metastasis, Method/Assay Development, Microenvironment, Oncogenic Stress, Other, Outreach, Platform Development, Training Material, Tumor Progression, Tumor-Immune, Computer Science, Environmental Science, Information Science, Educational Technology, Anatomy/Physiology, Biology, Ecology, Genetics, Nutrition, Measurement and Data, Statistics and Probability, Chemistry, Physics, Systems Biology",,TRUE,,,,OER,list like @@ -34,7 +35,7 @@ Resource Educational Level,"Educational context (pre-school, lower-primary, uppe Resource Description,Abstract or summary of the item.,,,TRUE,,,,OER,str Resource Origin Institution,Institution(s) of origin for this item. Multiple values should be provided as a comma separated list.,,,TRUE,,,,OER,list like Resource Language,Language of the item (not of the metadata). Multiple values should be provided as a comma separated list.,"aa, ab, ae, af, ak, am, an, ar, as, av, ay, az, ba, be, bg, bh, bi, bm, bn, bo, br, bs, ca, ca, ce, ch, co, cr, cs, cu, cv, cy, da, de, dv, dv, dz, ee, el, en, eo, es, et, eu, fa, ff, fi, fj, fo, fr, fy, ga, gd, gl, gn, gu, gv, ha, he, hi, ho, hr, ht, hu, hy, hz, ia, id, ie, ig, ii, ik, io, is, it, iu, ja, jv, ka, kg, ki, kj, kk, kl, km, kn, ko, kr, ks, ku, kv, kw, ky, la, lb, lg, li, ln, lo, lt, lu, lv, mg, mh, mi, mk, ml, mn, mr, ms, mt, my, na, nb, nd, ne, ng, nl, nn, no, nr, nv, ny, oc, oj, om, or, os, pa, pi, pl, ps, pt, qu, rm, rn, ro, ru, rw, sa, sc, sd, se, sg, si, sk, sl, sm, sn, so, sq, sr, ss, st, su, sv, sw, ta, te, tg, th, ti, tk, tl, tn, to, tr, ts, tt, tw, ty, ug, uk, ur, uz, ve, vi, vo, wa, wo, xh, yi, yo, za, zh, zu",,TRUE,,,,OER,list like :: regex fullmatch [a-z]{2} -Resource Contributors,The name(s) of the contributor(s) to the item. Multiple contributor names should be provided as a comma-separated list. ,,,TRUE,,,,OER,list like +Resource Contributors,The name(s) of the contributor(s) to the item. Multiple contributor names should be provided as a comma-separated list.,,,TRUE,,,,OER,list like Resource Grant Number,"The grant number(s) associated with the contributor(s) of the item. If no grant number listed is applicable, please select 'Affiliated/Non-Grant Associated'. Multiple values should be provided as a comma separated list.","Affiliated/Non-Grant Associated, CA184897, CA184898, CA188388, CA193313, CA193417, CA193419, CA193461, CA193489, CA195469, CA199315, CA202123, CA202144, CA202177, CA202229, CA202241, CA209891, CA209923, CA209971, CA209975, CA209978, CA209988, CA209992, CA209997, CA210152, CA210173, CA210180, CA210181, CA210184, CA210190, CA214282, CA214292, CA214297, CA214300, CA214354, CA214369, CA214381, CA214411, CA215709, CA215794, CA215798, CA215845, CA215848, CA217297, CA217376, CA217377, CA217378, CA217450, CA217456, CA217514, CA217613, CA217617, CA217655, CA220378, CA223976, CA224012, CA224013, CA224044, CA225088, CA225566, CA227136, CA227544, CA227550, CA228608, CA228963, CA231978, CA232137, CA232161, CA232209, CA232216, CA232382, CA232517, CA234787, CA235747, CA238475, CA238720, CA238728, CA240301, CA241137, CA241927, CA243004, CA243007, CA243072, CA243073, CA243075, CA244100, CA244101, CA244107, CA244109, CA245313, CA248890, CA249799, CA250040, CA250044, CA250046, CA250481, CA251443, CA253248, CA253472, CA253540, CA253547, CA253553, CA254200, CA254886, CA256054, CA256481, CA260432, CA261694, CA261701, CA261717, CA261719, CA261822, CA261841, CA261842, CA263001, CA264583, CA264610, CA264611, CA264620, CA267170, CA268069, CA268072, CA268083, CA268084, CA271273, CA274492, CA274494, CA274499, CA274502, CA274509, CA275808",,TRUE,,,,MC2/grant,list like Resource Secondary Topic,"Additional topics or keywords to describe the content of the item, in addition to the primary topic. Multiple values should be provided as a comma-separated list.",,,FALSE,,,,OER,list like Resource License,"The name of the license applied to the item by the contributor(s), if applicable. Multiple values should be provided as a comma separated list.","AAL, ADSL, AFL-1.1, AFL-1.2, AFL-2.0, AFL-2.1, AFL-3.0, AGPL-1.0, AGPL-3.0, AMDPLPA, AML, AMPAS, ANTLR-PD, APAFML, APL-1.0, APSL-1.0, APSL-1.1, APSL-1.2, APSL-2.0, Abstyles, Adobe-2006, Adobe-Glyph, Afmparse, Aladdin, Apache-1.0, Apache-1.1, Apache-2.0, Artistic-1.0, Artistic-1.0-Perl, Artistic-1.0-cl8, Artistic-2.0, BSD-2-Clause, BSD-2-Clause-FreeBSD, BSD-2-Clause-NetBSD, BSD-3-Clause, BSD-3-Clause-Attribution, BSD-3-Clause-Clear, BSD-3-Clause-LBNL, BSD-3-Clause-No-Nuclear-License, BSD-3-Clause-No-Nuclear-License-2014, BSD-3-Clause-No-Nuclear-Warranty, BSD-4-Clause, BSD-4-Clause-UC, BSD-Protection, BSD-Source-Code, BSD-style, BSL-1.0, Bahyph, Barr, Beerware, BitTorrent-1.0, BitTorrent-1.1, Borceux, CATOSL-1.1, CC-BY-1.0, CC-BY-2.0, CC-BY-2.5, CC-BY-3.0, CC-BY-4.0, CC-BY-NC-1.0, CC-BY-NC-2.0, CC-BY-NC-2.5, CC-BY-NC-3.0, CC-BY-NC-4.0, CC-BY-NC-ND-1.0, CC-BY-NC-ND-2.0, CC-BY-NC-ND-2.5, CC-BY-NC-ND-3.0, CC-BY-NC-ND-4.0, CC-BY-NC-SA-1.0, CC-BY-NC-SA-2.0, CC-BY-NC-SA-2.5, CC-BY-NC-SA-3.0, CC-BY-NC-SA-4.0, CC-BY-ND-1.0, CC-BY-ND-2.0, CC-BY-ND-2.5, CC-BY-ND-3.0, CC-BY-ND-4.0, CC-BY-SA-1.0, CC-BY-SA-2.0, CC-BY-SA-2.5, CC-BY-SA-3.0, CC-BY-SA-4.0, CC0-1.0, CDDL-1.0, CDDL-1.1, CECILL-1.0, CECILL-1.1, CECILL-2.0, CECILL-2.1, CECILL-B, CECILL-C, CNRI-Jython, CNRI-Python, CNRI-Python-GPL-Compatible, CPAL-1.0, CPL-1.0, CPOL-1.02, CUA-OPL-1.0, Caldera, ClArtistic, Condor-1.1, Crossword, CrystalStacker, Cube, D-FSL-1.0, DOC, DSDP, Dotseqn, ECL-1.0, ECL-2.0, EFL-1.0, EFL-2.0, EPL-1.0, EUDatagrid, EUPL-1.0, EUPL-1.1, Entessa, ErlPL-1.1, Eurosym, FSFAP, FSFUL, FSFULLR, FTL, Fair, Frameworx-1.0, FreeImage, Freeware, GFDL-1.1, GFDL-1.2, GFDL-1.3, GL2PS, GPL-1.0, GPL-2.0, GPL-3.0, Giftware, Glide, Glulxe, HPND, HaskellReport, IBM-pibs, ICU, IJG, IPA, IPL-1.0, ISC, ImageMagick, Imlib2, Info-ZIP, Intel, Intel-ACPI, Interbase-1.0, JSON, JasPer-2.0, LAL-1.2, LAL-1.3, LGPL-2.0, LGPL-2.1, LGPL-3.0, LGPLLR, LPL-1.0, LPL-1.02, LPPL-1.0, LPPL-1.1, LPPL-1.2, LPPL-1.3a, LPPL-1.3c, Latex2e, Leptonica, LiLiQ-P-1.1, LiLiQ-R-1.1, LiLiQ-Rplus-1.1, Libpng, MIT, MIT-CMU, MIT-advertising, MIT-enna, MIT-feh, MITNFA, MPL-1.0, MPL-1.1, MPL-2.0, MPL-2.0-no-copyleft-exception, MS-PL, MS-RL, MTLL, MakeIndex, MirOS, Motosoto, Multics, Mup, NASA-1.3, NBPL-1.0, NCSA, NGPL, NLOD-1.0, NLPL, NOSL, NPL-1.0, NPL-1.1, NPOSL-3.0, NRL, NTP, Naumen, NetCDF, Newsletr, Nokia, Not licensed, Noweb, Nunit, OCCT-PL, OCLC-2.0, ODbL-1.0, OFL-1.0, OFL-1.1, OGTSL, OLDAP-1.1, OLDAP-1.2, OLDAP-1.3, OLDAP-1.4, OLDAP-2.0, OLDAP-2.0.1, OLDAP-2.1, OLDAP-2.2, OLDAP-2.2.1, OLDAP-2.2.2, OLDAP-2.3, OLDAP-2.4, OLDAP-2.5, OLDAP-2.6, OLDAP-2.7, OLDAP-2.8, OML, OPL-1.0, OSET-PL-2.1, OSL-1.0, OSL-1.1, OSL-2.0, OSL-2.1, OSL-3.0, OpenSSL, Other, PDDL-1.0, PHP-3.0, PHP-3.01, Plexus, PostgreSQL, Proprietary, Python-2.0, QPL-1.0, Qhull, RHeCos-1.1, RPL-1.1, RPL-1.5, RPSL-1.0, RSA-MD, RSCPL, Rdisc, Ruby, SAX-PD, SCEA, SGI-B-1.0, SGI-B-1.1, SGI-B-2.0, SISSL, SISSL-1.2, SMLNJ, SMPPL, SNIA, SPL-1.0, SWL, Saxpath, Sendmail, SimPL-2.0, Sleepycat, Spencer-86, Spencer-94, Spencer-99, SugarCRM-1.1.3, TCL, TMate, TORQUE-1.1, TOSL, UPL-1.0, Unicode-TOU, Unlicense, VOSTROM, VSL-1.0, Vim, W3C, W3C-19980720, WTFPL, Watcom-1.0, Wsuipa, X11, XFree86-1.1, XSkat, Xerox, Xnet, YPL-1.0, YPL-1.1, ZPL-1.1, ZPL-2.0, ZPL-2.1, Zed, Zend-2.0, Zimbra-1.3, Zimbra-1.4, Zlib, bzip2-1.0.5, bzip2-1.0.6, curl, diffmark, dvipdfm, eGenix, gSOAP-1.3b, gnuplot, iMatix, libtiff, mpich2, psfrag, psutils, xinetd, xpp, zlib-acknowledgement",,FALSE,,,,OER,list like @@ -45,17 +46,19 @@ Resource Media Accessibility,"Accessibility features (Alternative Text, Audio De Resource Access Hazard,"Sensory hazards (Flashing, Motion, etc.) applicable to the item. Multiple values should be provided as a comma separated list.","Flashing, Motion, Simulation, Sound",,FALSE,,,,OER,list like Resource Dataset Alias,"URL or persistent identifier (DOI, Synapse ID) for any dataset(s) that is intended to be used with the item. Multiple values should be provided as a comma separated list.",,,FALSE,,,,MC2/dataset,list like Resource Tool Link,"URL or persistent identifier (DOI, Synapse ID) for any software or tool that is intended to be used with the item. Multiple values should be provided as a comma separated list.",,,FALSE,,,,MC2/tool,list like +EducationalResource_id,A unique primary key that enables record updates using schematic.,,,TRUE,,,,,unique Grant,Consortium grant information,,"Component, Grant Name, Grant Number, Grant Abstract, Grant Type",FALSE,,,,, Grant Name,Name of the grant,,,TRUE,,,,, Grant Number,"Number of the grant (i.e. ""CA------"" format)",,,TRUE,,,,,regex search ^CA\d{6}$ Grant Abstract,Abstract for the grant,,,TRUE,,,,, Grant Type,Type of grant,"R01, R21, R37, U01, U24, U54",,TRUE,,,,, -Grant View,The denormalized manifest for grant submission.,,"Component, Grant Name, Grant Number, Grant Abstract, Grant Type, Grant Theme Name, Grant Institution Name, Grant Institution Alias, Grant Investigator, Grant Consortium Name",FALSE,,,"Theme, Institution, Consortium, Grant",, +Grant View,The denormalized manifest for grant submission.,,"Component, GrantView_id, Grant Name, Grant Number, Grant Abstract, Grant Type, Grant Theme Name, Grant Institution Name, Grant Institution Alias, Grant Investigator, Grant Consortium Name",FALSE,,,"Theme, Institution, Consortium, Grant",, Grant Theme Name,Theme(s) associated with the grant. 1...*,"Computational Model Development, Computational Resource, Drug Resistance/Sensitivity, Epigenetics, Evolution, Experimental Model Development, Heterogeneity, Immunotherapy, Mechano-genetics, Mechano-resistance, Metabolism, Metastasis, Method/Assay Development, Microenvironment, Oncogenic Stress, Platform Development, Tumor Progression, Tumor-Immune",,TRUE,,,,,list like Grant Institution Name,The full name of the institution(s) associated with the grant. (e.g. Harvard University). 1...*,"Arizona State University, Auburn University, Barrow Neurological Institute, Baylor College Of Medicine, Beth Israel Deaconess Hospital, Boston Medical Center, Boston University, Brigham and Womens Hospital, California Institute of Technology, Childrens Hospital of Philadelphia, City Of Hope, Cleveland Clinic, Cold Spring Harbor Laboratory, Columbia University, Cornell University, Dana-Farber Cancer Institute, Dartmouth College, Duke University, Emory University, Georgia Institute of Technology, Harvard Medical School, Harvard University, Hebrew University of Jerusalem, Houston Methodist, Indiana University, Indiana University - Purdue University Indianapolis, Institute for Systems Biology, Jackson Laboratory, Johns Hopkins University, Lurie Children's Hospital, Massachusetts General Hospital, Massachusetts Institute of Technology, Mayo Clinic, Memorial Sloan Kettering Cancer Center, Moffitt Cancer Center, New York University, Northwestern University, Oregon Health & Science University, Pacific Northwest National Laboratory, Rockefeller University, Sage Bionetworks, Salk Institute for Biological Studies, St. Jude Children's Research Hospital, Stanford University, Stony Brook University, The University of Texas Health Science Center at San Antonio, University of Alabama at Birmingham, University of Arizona, University of California; Berkeley, University of California; Irvine, University of California; Los Angeles, University of California; San Diego, University of California; San Francisco, University of Chicago, University of Chicago Medical Center, University of Colorado Denver, University of Delaware, University of Florida, University of Illinois, University of Illinois at Chicago, University of Massachusetts Medical School, University of Miami, University of Michigan, University of Minnesota, University of New South Wales, University of North Carolina at Chapel Hill, University of Pennsylvania, University of Pittsburgh, University of Southern California, University of Texas MD Anderson Cancer Center, University of Texas Southwestern Medical Center, University of Texas at Austin, University of Utah, University of Virginia, University of Washington, University of Wisconsin-Madison, Vanderbilt University, Wake Forest, Weill Cornell Medicine, Wistar Institute, Yale University",,TRUE,,,,,list like Grant Institution Alias,The alias of the institution(s) associated with the grant (e.g. UCSD). 1...*,"ASU, AU, BCM, BIDMC, BMC, BU, BWH, Barrow, CHOP, COH, CSHL, Caltech, Cleveland Clinic, Columbia, Cornell, DFCI, Dartmouth, Duke, Emory, GTech, HMS, HUJI, Harvard, Houston Methodist, ISB, IU, IUPUI, JHU, Jackson Laboratory, Lurie Children's Hospital, MGH, MIT, MSKCC, Mayo, Moffitt, NU, NYU, OHSU, PNNL, Pitt, Rockefeller University, SBU, Sage, Salk, StJude, Stanford, U Miami, UA, UAB, UCBerkeley, UCD, UCI, UCLA, UCMC, UCSD, UCSF, UChicago, UD, UFL, UIC, UMMS, UMichigan, UMinn, UNC, UNSW, UPenn, USC, UT Austin, UT Southwestern, UTHSCSA, UUtah, UVA, UW, UWM, University of Illinois, University of Texas MD Anderson Cancer Center, Vanderbilt, WCM, Wake Forest, Wistar, Yale",,TRUE,,,,,list like Grant Investigator,Investigator(s) associated witht the grant. 1...*,,,TRUE,,,,,list like Grant Consortium Name,Consortium(s) associated with the grant. 1...1,"CCBIR, CSBC, HTAN, ICBP, MetNet, NCI, NCI Clinical and Translational Exploratory/Developmental Studies, PDMC, PS-ON, Sage Bionetworks, TEC",,TRUE,,,,, +GrantView_id,A unique primary key that enables record updates using schematic.,,,TRUE,,,,,unique Institution,Institutions participating in consortia activities,,"Component, Institution Name, Institution Full Name, Institution Alias, Institution Location State, Institution Location City, Rorid",FALSE,,,,, Institution Name,"Machine readable name of the institution. (e.g. ArizonaStatUniversity, BostonUniversity, etc.)",,,TRUE,,,,, Institution Full Name,"Human readable, full name of the institution. (e.g. Arizona State University, Boston University, etc.)",,,TRUE,,,,, @@ -77,22 +80,24 @@ Chair Roles,"Committee or working group chair role(s) the individual fulfilled ( Consent For Portal Display,Consent from individual to display Person information in the CCKP,"No, Yes",,TRUE,,,,, Portal Display,Display content in CCKP,"FALSE, TRUE",,TRUE,,,,, Person Consortium,"Consortiums associated with a person, joined by uuids from the person and consortium table.",,"Component, Person, Consortium",FALSE,,,"Person, Consortium",, -Person View,The denormalized manifest for person submission.,,"Component, Person Grant Number, Person Consortium Name, Name, Alternative Names, Email, Url, Orcid Id, Synapse Profile Id, Last Known Institution, Working Group Participation, Chair Roles, Consent For Portal Display, Portal Display, Person Publications, Person Datasets, Person Tools, Person Educational Resources",FALSE,,,"Publication, Dataset, Tool, Consortium, Grant, Person, Educational Resource",, +Person View,The denormalized manifest for person submission.,,"Component, PersonView_id, Person Grant Number, Person Consortium Name, Name, Alternative Names, Email, Url, Orcid Id, Synapse Profile Id, Last Known Institution, Working Group Participation, Chair Roles, Consent For Portal Display, Portal Display, Person Publications, Person Datasets, Person Tools, Person Educational Resources",FALSE,,,"Publication, Dataset, Tool, Consortium, Grant, Person, Educational Resource",, Person Grant Number,"Grant number(s) associated with the person. Multiple values permitted, comma separated.","Affiliated/Non-Grant Associated, CA184897, CA184898, CA188388, CA193313, CA193417, CA193419, CA193461, CA193489, CA195469, CA199315, CA202123, CA202144, CA202177, CA202229, CA202241, CA209891, CA209923, CA209971, CA209975, CA209978, CA209988, CA209992, CA209997, CA210152, CA210173, CA210180, CA210181, CA210184, CA210190, CA214282, CA214292, CA214297, CA214300, CA214354, CA214369, CA214381, CA214411, CA215709, CA215794, CA215798, CA215845, CA215848, CA217297, CA217376, CA217377, CA217378, CA217450, CA217456, CA217514, CA217613, CA217617, CA217655, CA220378, CA223976, CA224012, CA224013, CA224044, CA225088, CA225566, CA227136, CA227544, CA227550, CA228608, CA228963, CA231978, CA232137, CA232161, CA232209, CA232216, CA232382, CA232517, CA234787, CA235747, CA238475, CA238720, CA238728, CA240301, CA241137, CA241927, CA243004, CA243007, CA243072, CA243073, CA243075, CA244100, CA244101, CA244107, CA244109, CA245313, CA248890, CA249799, CA250040, CA250044, CA250046, CA250481, CA251443, CA253248, CA253472, CA253540, CA253547, CA253553, CA254200, CA254886, CA256054, CA256481, CA260432, CA261694, CA261701, CA261717, CA261719, CA261822, CA261841, CA261842, CA263001, CA264583, CA264610, CA264611, CA264620, CA267170, CA268069, CA268072, CA268083, CA268084, CA271273, CA274492, CA274494, CA274499, CA274502, CA274509, CA275808",,TRUE,,,,,list like Person Consortium Name,"Consortium(s) associated with the person. Multiple values permitted, comma separated.","CCBIR, CSBC, HTAN, ICBP, MetNet, NCI, NCI Clinical and Translational Exploratory/Developmental Studies, PDMC, PS-ON, Sage Bionetworks, TEC",,TRUE,,,,,list like Person Publications,"A list of the pubmed Ids associated with the person. Multiple values permitted, comma separated.",,,FALSE,,,,,list like Person Datasets,"A list of the dataset aliases (An alias of the dataset must be unique. Can be the GEO identifier such as GSE12345, or a DOI. No Greek Letters) associated with the person. Multiple values permitted, comma separated.",,,FALSE,,,,,list like Person Tools,"A list of the tool names associated with the person. Multiple values permitted, comma separated.",,,FALSE,,,,,list like Person Educational Resources,"A list of educational resource identifiers associated with the person. Multiple values permitted, comma separated.",,,FALSE,,,,,list like +PersonView_id,A unique primary key that enables record updates using schematic.,,,TRUE,,,,,unique Project,Projects associated with consortia grants,,"Component, Project Name, Project Type, Project Description",FALSE,,,Grant,, Project Name,Name of the project,,,TRUE,,,,, Project Type,Type of project,"Core, Project",,TRUE,,,,, Project Description,Description of the project,,,TRUE,,,,, Project Investigator,Investigator(s) associated witht the project. 1...*,,,TRUE,,,,,list like -Project View,The denormalized manifest for project submission.,,"Component, Project Name, Project Type, Project Description, Project Investigator, Project Consortium Name, Project Grant Number",FALSE,,,"Project, Grant",, +Project View,The denormalized manifest for project submission.,,"Component, ProjectView_id, Project Name, Project Type, Project Description, Project Investigator, Project Consortium Name, Project Grant Number",FALSE,,,"Project, Grant",, Project Grant Number,Grant number(s) associated with the project 1...*,"Affiliated/Non-Grant Associated, CA184897, CA184898, CA188388, CA193313, CA193417, CA193419, CA193461, CA193489, CA195469, CA199315, CA202123, CA202144, CA202177, CA202229, CA202241, CA209891, CA209923, CA209971, CA209975, CA209978, CA209988, CA209992, CA209997, CA210152, CA210173, CA210180, CA210181, CA210184, CA210190, CA214282, CA214292, CA214297, CA214300, CA214354, CA214369, CA214381, CA214411, CA215709, CA215794, CA215798, CA215845, CA215848, CA217297, CA217376, CA217377, CA217378, CA217450, CA217456, CA217514, CA217613, CA217617, CA217655, CA220378, CA223976, CA224012, CA224013, CA224044, CA225088, CA225566, CA227136, CA227544, CA227550, CA228608, CA228963, CA231978, CA232137, CA232161, CA232209, CA232216, CA232382, CA232517, CA234787, CA235747, CA238475, CA238720, CA238728, CA240301, CA241137, CA241927, CA243004, CA243007, CA243072, CA243073, CA243075, CA244100, CA244101, CA244107, CA244109, CA245313, CA248890, CA249799, CA250040, CA250044, CA250046, CA250481, CA251443, CA253248, CA253472, CA253540, CA253547, CA253553, CA254200, CA254886, CA256054, CA256481, CA260432, CA261694, CA261701, CA261717, CA261719, CA261822, CA261841, CA261842, CA263001, CA264583, CA264610, CA264611, CA264620, CA267170, CA268069, CA268072, CA268083, CA268084, CA271273, CA274492, CA274494, CA274499, CA274502, CA274509, CA275808",,TRUE,,,,,list like Project Consorium Name, Consortium(s) associated with the project. 1...1,,,TRUE,,,,, -Project Consortium Name,,"CCBIR, CSBC, HTAN, ICBP, MetNet, NCI, NCI Clinical and Translational Exploratory/Developmental Studies, PDMC, PS-ON, Sage Bionetworks, TEC",,,,,,, +Project Consortium Name,,"CCBIR, CSBC, HTAN, ICBP, MetNet, NCI, NCI Clinical and Translational Exploratory/Developmental Studies, PDMC, PS-ON, Sage Bionetworks, TEC",,TRUE,,,,, +ProjectView_id,A unique primary key that enables record updates using schematic.,,,TRUE,,,,,unique Publication,Publication derived from consortia activity,,"Component, Publication Doi, Publication Journal, Pubmed Id, Pubmed Id, Pubmed Url, Publication Title, Publication Year, Publication Keywords, Publication Authors, Publication Abstract, Publication Assay, Publication Tumor Type, Publication Tissue, Publication Accessibility",FALSE,,,,, Publication Doi,The digital object identifier associated with the publication in the form of https://www.doi.org/{doi} to comply with CrossRef DOI display guidelines.,,,FALSE,,,,,unique Publication Journal,The name of the periodical publication in which the publication was published.,,,TRUE,,,,, @@ -108,11 +113,12 @@ Publication Tumor Type,"Tumor type(s) associated with the publication. Multiple Publication Tissue,"Tissue type(s) associated with the publication. Multiple values permitted, comma separated.","Gonad, Abdominal Esophagus, Adipose Tissue, Adrenal Gland, Alveolus, Aorta, Artery, Ascending Colon, Bile Duct, Bladder, Blood, Blood Vessel, Bone, Bone Marrow, Brain, Breast, Caecum, Cancer-Associated Fibroblast, Cardia, Cartilage, Cervix Uteri, Choroid, Colon, Connective and Soft Tissue, Cornea, Duodenum, Ear, Embryo, Embryonic Heart, Endocervix, Endometrium, Endothelium, Epithelium, Esophagus, Eye, Fallopian Tube, Foreskin, Frontal Lobe, Gastroesophageal Junction, Gastrointestinal Tract, Genitourinary, Hair Follicle, Head and Neck, Heart, Heart Muscle, Hematopoietic System, Hippocampus, Intestine, Intra-Abdominal Lymph Nodes, Intrathoracic Lymph Nodes, Joint, Kidney, Larynx, Ligament, Liver, Lung, Lymph, Lymph Node, Lymph Nodes of Axilla or Arm, Lymph Nodes of Inguinal Region or Leg, Lymphatic System, Lymphoid Tissue, Main Bronchus, Mammary Gland, Meninges, Mesenchyme, Mucosa, Muscle, Nasal Cavity, Nervous System, Not Applicable, Olfactory Mucosa, Omentum, Oral Cavity, Oral Mucosa, Ovary, Pancreas, Pelvic Lymph Nodes, Pending Annotation, Periodontal Ligament, Peripheral Nerves, Peritoneum, Pharynx, Pituitary Gland, Placenta, Pleura, Prostate Gland, Rectum, Reproductive System, Respiratory System, Salivary Gland, Sclera, Sinonasal Tract, Skin, Small Intestine, Spinal Cord, Spleen, Stomach, Synovial Membrane, Tendon, Testis, Thymus, Thyroid Gland, Tongue, Tonsil, Trachea, Umbilical Cord, Unspecified, Uterus, Vagina, Vascular Endothelium, Vein, Vertebra, Peripheral Blood Mononuclear Cell",,TRUE,,,,,list like Publication Accessibility,Whether there are non-monetary restrictions on accessing an the publication.,"Open Access, Restricted Access",,TRUE,,,,, Publication Grant,"Publications associated with a grant, joined by uuids from the publication and grant table. ",,"Component, Publication, Grant",FALSE,,,"Publication, Grant",, -Publication View,The denormalized manifest for publication submission.,,"Component, Publication Grant Number, Publication Doi, Publication Journal, Pubmed Id, Pubmed Url, Publication Title, Publication Year, Publication Keywords, Publication Authors, Publication Abstract, Publication Assay, Publication Tumor Type, Publication Tissue, Publication Accessibility, Publication Dataset Alias",FALSE,,,"Dataset, Tool, Grant, Publication",, +Publication View,The denormalized manifest for publication submission.,,"Component, PublicationView_id, Publication Grant Number, Publication Doi, Publication Journal, Pubmed Id, Pubmed Url, Publication Title, Publication Year, Publication Keywords, Publication Authors, Publication Abstract, Publication Assay, Publication Tumor Type, Publication Tissue, Publication Accessibility, Publication Dataset Alias",FALSE,,,"Dataset, Tool, Grant, Publication",, Publication Grant Number,"Relevant grant number associated witht the publication's development. Multiple values permitted, comma separated.","Affiliated/Non-Grant Associated, CA184897, CA184898, CA188388, CA193313, CA193417, CA193419, CA193461, CA193489, CA195469, CA199315, CA202123, CA202144, CA202177, CA202229, CA202241, CA209891, CA209923, CA209971, CA209975, CA209978, CA209988, CA209992, CA209997, CA210152, CA210173, CA210180, CA210181, CA210184, CA210190, CA214282, CA214292, CA214297, CA214300, CA214354, CA214369, CA214381, CA214411, CA215709, CA215794, CA215798, CA215845, CA215848, CA217297, CA217376, CA217377, CA217378, CA217450, CA217456, CA217514, CA217613, CA217617, CA217655, CA220378, CA223976, CA224012, CA224013, CA224044, CA225088, CA225566, CA227136, CA227544, CA227550, CA228608, CA228963, CA231978, CA232137, CA232161, CA232209, CA232216, CA232382, CA232517, CA234787, CA235747, CA238475, CA238720, CA238728, CA240301, CA241137, CA241927, CA243004, CA243007, CA243072, CA243073, CA243075, CA244100, CA244101, CA244107, CA244109, CA245313, CA248890, CA249799, CA250040, CA250044, CA250046, CA250481, CA251443, CA253248, CA253472, CA253540, CA253547, CA253553, CA254200, CA254886, CA256054, CA256481, CA260432, CA261694, CA261701, CA261717, CA261719, CA261822, CA261841, CA261842, CA263001, CA264583, CA264610, CA264611, CA264620, CA267170, CA268069, CA268072, CA268083, CA268084, CA271273, CA274492, CA274494, CA274499, CA274502, CA274509, CA275808",,TRUE,,,,,list like Publication Dataset Alias,"A list of the dataset aliases (An alias of the dataset must be unique. Can be the GEO identifier such as GSE12345, or a DOI. No Greek Letters) associated with the publication. Multiple values permitted, comma separated.",,,FALSE,,,,,list like Publication View DCA,The denormalized manifest for publication submission with component_id field for DCA upsert function.,,"Component, PublicationViewDCA_id, Publication Grant Number, Publication Doi, Publication Journal, Pubmed Id, Pubmed Url, Publication Title, Publication Year, Publication Keywords, Publication Authors, Publication Abstract, Publication Assay, Publication Tumor Type, Publication Tissue, Publication Accessibility, Publication Dataset Alias",FALSE,,,"Dataset, Tool, Grant, Publication",, PublicationViewDCA_id,Unique identifier that allows schematic to update and insert entries.,,,TRUE,,,,,unique +PublicationView_id,A unique primary key that enables record updates using schematic.,,,TRUE,,,,,unique Component,"Category of metadata (e.g. Tools, Publications, etc.); provide the same one for all items/rows.",,,TRUE,,,,, Theme,Themes associated with resources derived from consortia activities,,"Component, Theme Name, Theme Display Name, Theme Description",FALSE,,,,, Theme Name,"Machine readable name of the research theme. (e.g. compuational_resource, drug_resistance_sensitivity).",,,TRUE,,,,, @@ -149,6 +155,7 @@ Tool Link Url,A link of some relevance to the software (URL).,,,FALSE,,,,biotool Tool Link Type,"The type of data, information or system that is obtained when the link is resolved. Multiple values permitted, comma separated.","Discussion Forum, Galaxy Service, Helpdesk, Issue Tracker, Mailing list, Mirror, Other, Repository, Service, Social Media, Software Catalogue, Technical Monitoring",,FALSE,,,,biotoolsschema,list like Tool Link Note,Comment about the link.,,,FALSE,,,,biotoolsschema, Tool Grant,"Tools associated with a grant, joined by uuids from the tool table and grant table.",,"Component, Tool, Grant",FALSE,,,"Tool, Grant",, -Tool View,The denormalized manifest for tool submission.,,"Component, Tool Pubmed Id, Tool Grant Number, Tool Name, Tool Description, Tool Homepage, Tool Version, Tool Operation, Tool Input Data, Tool Output Data, Tool Input Format, Tool Output Format, Tool Function Note, Tool Cmd, Tool Type, Tool Topic, Tool Operating System, Tool Language, Tool License, Tool Cost, Tool Accessibility, Tool Download Url, Tool Download Type, Tool Download Note, Tool Download Version, Tool Documentation Url, Tool Documentation Type, Tool Documentation Note, Tool Link Url, Tool Link Type, Tool Link Note",FALSE,,,"Publication, Dataset, Grant, Tool",, +Tool View,The denormalized manifest for tool submission.,,"Component, ToolView_id, Tool Pubmed Id, Tool Grant Number, Tool Name, Tool Description, Tool Homepage, Tool Version, Tool Operation, Tool Input Data, Tool Output Data, Tool Input Format, Tool Output Format, Tool Function Note, Tool Cmd, Tool Type, Tool Topic, Tool Operating System, Tool Language, Tool License, Tool Cost, Tool Accessibility, Tool Download Url, Tool Download Type, Tool Download Note, Tool Download Version, Tool Documentation Url, Tool Documentation Type, Tool Documentation Note, Tool Link Url, Tool Link Type, Tool Link Note",FALSE,,,"Publication, Dataset, Grant, Tool",, Tool Grant Number,"Grant number associated with the tool's development. Multiple values permitted, comma separated.","Affiliated/Non-Grant Associated, CA184897, CA184898, CA188388, CA193313, CA193417, CA193419, CA193461, CA193489, CA195469, CA199315, CA202123, CA202144, CA202177, CA202229, CA202241, CA209891, CA209923, CA209971, CA209975, CA209978, CA209988, CA209992, CA209997, CA210152, CA210173, CA210180, CA210181, CA210184, CA210190, CA214282, CA214292, CA214297, CA214300, CA214354, CA214369, CA214381, CA214411, CA215709, CA215794, CA215798, CA215845, CA215848, CA217297, CA217376, CA217377, CA217378, CA217450, CA217456, CA217514, CA217613, CA217617, CA217655, CA220378, CA223976, CA224012, CA224013, CA224044, CA225088, CA225566, CA227136, CA227544, CA227550, CA228608, CA228963, CA231978, CA232137, CA232161, CA232209, CA232216, CA232382, CA232517, CA234787, CA235747, CA238475, CA238720, CA238728, CA240301, CA241137, CA241927, CA243004, CA243007, CA243072, CA243073, CA243075, CA244100, CA244101, CA244107, CA244109, CA245313, CA248890, CA249799, CA250040, CA250044, CA250046, CA250481, CA251443, CA253248, CA253472, CA253540, CA253547, CA253553, CA254200, CA254886, CA256054, CA256481, CA260432, CA261694, CA261701, CA261717, CA261719, CA261822, CA261841, CA261842, CA263001, CA264583, CA264610, CA264611, CA264620, CA267170, CA268069, CA268072, CA268083, CA268084, CA271273, CA274492, CA274494, CA274499, CA274502, CA274509, CA275808",,TRUE,,,,,list like Tool Pubmed Id,The pubMed identifer associated with the development of the tool.,,,FALSE,,,,,int +ToolView_id,A unique primary key that enables record updates using schematic.,,,TRUE,,,,,unique diff --git a/mc2.model.jsonld b/mc2.model.jsonld index 78c4380..96aca92 100644 --- a/mc2.model.jsonld +++ b/mc2.model.jsonld @@ -4768,6 +4768,9 @@ { "@id": "bts:Component" }, + { + "@id": "bts:DatasetViewId" + }, { "@id": "bts:DatasetPubmedId" }, @@ -5240,6 +5243,25 @@ "list like" ] }, + { + "@id": "bts:DatasetViewId", + "@type": "rdfs:Class", + "rdfs:comment": "A unique primary key that enables record updates using schematic.", + "rdfs:label": "DatasetViewId", + "rdfs:subClassOf": [ + { + "@id": "schema:Thing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "DatasetView_id", + "sms:required": "sms:true", + "sms:validationRules": [ + "unique" + ] + }, { "@id": "bts:EducationalResource", "@type": "rdfs:Class", @@ -5270,6 +5292,9 @@ { "@id": "bts:Component" }, + { + "@id": "bts:EducationalResourceId" + }, { "@id": "bts:ResourceTitle" }, @@ -6391,7 +6416,7 @@ { "@id": "bts:ResourceContributors", "@type": "rdfs:Class", - "rdfs:comment": "The name(s) of the contributor(s) to the item. Multiple contributor names should be provided as a comma-separated list. ", + "rdfs:comment": "The name(s) of the contributor(s) to the item. Multiple contributor names should be provided as a comma-separated list.", "rdfs:label": "ResourceContributors", "rdfs:subClassOf": [ { @@ -8042,6 +8067,25 @@ "list like" ] }, + { + "@id": "bts:EducationalResourceId", + "@type": "rdfs:Class", + "rdfs:comment": "A unique primary key that enables record updates using schematic.", + "rdfs:label": "EducationalResourceId", + "rdfs:subClassOf": [ + { + "@id": "schema:Thing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "EducationalResource_id", + "sms:required": "sms:true", + "sms:validationRules": [ + "unique" + ] + }, { "@id": "bts:Grant", "@type": "rdfs:Class", @@ -8199,6 +8243,9 @@ { "@id": "bts:Component" }, + { + "@id": "bts:GrantViewId" + }, { "@id": "bts:GrantName" }, @@ -8903,6 +8950,25 @@ "sms:required": "sms:true", "sms:validationRules": [] }, + { + "@id": "bts:GrantViewId", + "@type": "rdfs:Class", + "rdfs:comment": "A unique primary key that enables record updates using schematic.", + "rdfs:label": "GrantViewId", + "rdfs:subClassOf": [ + { + "@id": "schema:Thing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "GrantView_id", + "sms:required": "sms:true", + "sms:validationRules": [ + "unique" + ] + }, { "@id": "bts:Institution", "@type": "rdfs:Class", @@ -9648,6 +9714,9 @@ { "@id": "bts:Component" }, + { + "@id": "bts:PersonViewId" + }, { "@id": "bts:PersonGrantNumber" }, @@ -10246,6 +10315,25 @@ "list like" ] }, + { + "@id": "bts:PersonViewId", + "@type": "rdfs:Class", + "rdfs:comment": "A unique primary key that enables record updates using schematic.", + "rdfs:label": "PersonViewId", + "rdfs:subClassOf": [ + { + "@id": "schema:Thing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "PersonView_id", + "sms:required": "sms:true", + "sms:validationRules": [ + "unique" + ] + }, { "@id": "bts:Project", "@type": "rdfs:Class", @@ -10387,6 +10475,9 @@ { "@id": "bts:Component" }, + { + "@id": "bts:ProjectViewId" + }, { "@id": "bts:ProjectName" }, @@ -10888,9 +10979,28 @@ } ], "sms:displayName": "Project Consortium Name", - "sms:required": "sms:false", + "sms:required": "sms:true", "sms:validationRules": [] }, + { + "@id": "bts:ProjectViewId", + "@type": "rdfs:Class", + "rdfs:comment": "A unique primary key that enables record updates using schematic.", + "rdfs:label": "ProjectViewId", + "rdfs:subClassOf": [ + { + "@id": "schema:Thing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "ProjectView_id", + "sms:required": "sms:true", + "sms:validationRules": [ + "unique" + ] + }, { "@id": "bts:Publication", "@type": "rdfs:Class", @@ -13181,6 +13291,9 @@ { "@id": "bts:Component" }, + { + "@id": "bts:PublicationViewId" + }, { "@id": "bts:PublicationGrantNumber" }, @@ -13765,6 +13878,25 @@ "unique" ] }, + { + "@id": "bts:PublicationViewId", + "@type": "rdfs:Class", + "rdfs:comment": "A unique primary key that enables record updates using schematic.", + "rdfs:label": "PublicationViewId", + "rdfs:subClassOf": [ + { + "@id": "schema:Thing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "PublicationView_id", + "sms:required": "sms:true", + "sms:validationRules": [ + "unique" + ] + }, { "@id": "bts:Component", "@type": "rdfs:Class", @@ -18300,6 +18432,9 @@ { "@id": "bts:Component" }, + { + "@id": "bts:ToolViewId" + }, { "@id": "bts:ToolPubmedId" }, @@ -18826,6 +18961,25 @@ "int" ] }, + { + "@id": "bts:ToolViewId", + "@type": "rdfs:Class", + "rdfs:comment": "A unique primary key that enables record updates using schematic.", + "rdfs:label": "ToolViewId", + "rdfs:subClassOf": [ + { + "@id": "schema:Thing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "ToolView_id", + "sms:required": "sms:true", + "sms:validationRules": [ + "unique" + ] + }, { "@id": "bts:NIH", "@type": "rdfs:Class", diff --git a/modules/person/annotationProperty.csv b/modules/person/annotationProperty.csv index dbb6b85..a0645dd 100644 --- a/modules/person/annotationProperty.csv +++ b/modules/person/annotationProperty.csv @@ -5,7 +5,7 @@ Alternative Names,"Other ways the individual's name is displayed. Multiple value Email,Email address of the individual,,,FALSE,,,,, Url,"URL, e.g., individual's home page address",,,FALSE,,,,, Orcid Id,Unique identifier (ORCID ID) of the individual,,,FALSE,,,,,regex search \d{4}\-\d{4}\-\d{4}\-\d{3}(\d|X) -Synapse Profile Id,"Unique identifier (Synapse Profile ID) of the individual. See identifer in the url of the synapse profile page. ",,,FALSE,,,,,unique +Synapse Profile Id,Unique identifier (Synapse Profile ID) of the individual. See identifer in the url of the synapse profile page. ,,,FALSE,,,,,unique Last Known Institution,Last known institutional affiliation of the individual.,,,TRUE,,,,, Working Group Participation,"CSBC/PSON working group(s) of which the individual is a member (current and former). Multiple values permitted, comma separated.","Cancer Metabolism, Cell and Tissue Mechanics, Education and Outreach, Image Analysis, Navigating Cancer with Science and Art, None, Patient Advocacy Working Group, Protein-Protein Interactions, Resource and Data Sharing",,TRUE,,,,,list like Chair Roles,"Committee or working group chair role(s) the individual fulfilled (current and former). Multiple values permitted, comma separated.","Annual Meeting, None, Steering Committee, Working Group",,TRUE,,,,,list like diff --git a/modules/project/annotationProperty.csv b/modules/project/annotationProperty.csv index 13b0a34..44feb7e 100644 --- a/modules/project/annotationProperty.csv +++ b/modules/project/annotationProperty.csv @@ -6,6 +6,6 @@ Project Description,Description of the project,,,TRUE,,,,, Project Investigator,Investigator(s) associated witht the project. 1...*,,,TRUE,,,,,list like Project View,The denormalized manifest for project submission.,,"Component, ProjectView_id, Project Name, Project Type, Project Description, Project Investigator, Project Consortium Name, Project Grant Number",FALSE,,,"Project, Grant",, Project Grant Number,Grant number(s) associated with the project 1...*,"Affiliated/Non-Grant Associated, CA184897, CA184898, CA188388, CA193313, CA193417, CA193419, CA193461, CA193489, CA195469, CA199315, CA202123, CA202144, CA202177, CA202229, CA202241, CA209891, CA209923, CA209971, CA209975, CA209978, CA209988, CA209992, CA209997, CA210152, CA210173, CA210180, CA210181, CA210184, CA210190, CA214282, CA214292, CA214297, CA214300, CA214354, CA214369, CA214381, CA214411, CA215709, CA215794, CA215798, CA215845, CA215848, CA217297, CA217376, CA217377, CA217378, CA217450, CA217456, CA217514, CA217613, CA217617, CA217655, CA220378, CA223976, CA224012, CA224013, CA224044, CA225088, CA225566, CA227136, CA227544, CA227550, CA228608, CA228963, CA231978, CA232137, CA232161, CA232209, CA232216, CA232382, CA232517, CA234787, CA235747, CA238475, CA238720, CA238728, CA240301, CA241137, CA241927, CA243004, CA243007, CA243072, CA243073, CA243075, CA244100, CA244101, CA244107, CA244109, CA245313, CA248890, CA249799, CA250040, CA250044, CA250046, CA250481, CA251443, CA253248, CA253472, CA253540, CA253547, CA253553, CA254200, CA254886, CA256054, CA256481, CA260432, CA261694, CA261701, CA261717, CA261719, CA261822, CA261841, CA261842, CA263001, CA264583, CA264610, CA264611, CA264620, CA267170, CA268069, CA268072, CA268083, CA268084, CA271273, CA274492, CA274494, CA274499, CA274502, CA274509, CA275808",,TRUE,,,,,list like -Project Consorium Name," Consortium(s) associated with the project. 1...1",,,TRUE,,,,, +Project Consorium Name, Consortium(s) associated with the project. 1...1,,,TRUE,,,,, Project Consortium Name,,"CCBIR, CSBC, HTAN, ICBP, MetNet, NCI, NCI Clinical and Translational Exploratory/Developmental Studies, PDMC, PS-ON, Sage Bionetworks, TEC",,TRUE,,,,, ProjectView_id,A unique primary key that enables record updates using schematic.,,,TRUE,,,,,unique