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==Data from publications== | ==Data from publications== | ||
- | The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of Nov. | + | The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of Nov. 26, 2017. |
#Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD, (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [http://gpmdb.org/data/keyword/12177431 498]. | #Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD, (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [http://gpmdb.org/data/keyword/12177431 498]. | ||
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#Dittus L, Werner T, Muelbaier M, Bantscheff M, (2017) "Differential Kinobeads Profiling for Target Identification of Irreversible Kinase Inhibitors." <i>ACS Chem Biol</i> <b>12</b>(10):2515–2521; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28876896 28876896]; doi: [https://dx.doi.org/10.1021/acschembio.7b00617 10.1021/acschembio.7b00617]; GPMDB: [http://gpmdb.org/data/keyword/28876896 154]. | #Dittus L, Werner T, Muelbaier M, Bantscheff M, (2017) "Differential Kinobeads Profiling for Target Identification of Irreversible Kinase Inhibitors." <i>ACS Chem Biol</i> <b>12</b>(10):2515–2521; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28876896 28876896]; doi: [https://dx.doi.org/10.1021/acschembio.7b00617 10.1021/acschembio.7b00617]; GPMDB: [http://gpmdb.org/data/keyword/28876896 154]. | ||
#Kälin S, Becker M, Ott VB, Serr I, Hosp F, Mollah MMH, Keipert S, Lamp D, Rohner-Jeanrenaud F, Flynn VK, Scherm MG, Nascimento LFR, Gerlach K, Popp V, Dietzen S, Bopp T, Krishnamurthy P, Kaplan MH, Serrano M, Woods SC, Tripal P, Palmisano R, Jastroch M, Blüher M, Wolfrum C, Weigmann B, Ziegler AG, Mann M, Tschöp MH, Daniel C, (2017) "A Stat6/Pten Axis Links Regulatory T Cells with Adipose Tissue Function." <i>Cell Metab</i> <b>26</b>(3):475–492.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28877454 28877454]; doi: [https://dx.doi.org/10.1016/j.cmet.2017.08.008 10.1016/j.cmet.2017.08.008]; GPMDB: [http://gpmdb.org/data/keyword/28877454 31]. | #Kälin S, Becker M, Ott VB, Serr I, Hosp F, Mollah MMH, Keipert S, Lamp D, Rohner-Jeanrenaud F, Flynn VK, Scherm MG, Nascimento LFR, Gerlach K, Popp V, Dietzen S, Bopp T, Krishnamurthy P, Kaplan MH, Serrano M, Woods SC, Tripal P, Palmisano R, Jastroch M, Blüher M, Wolfrum C, Weigmann B, Ziegler AG, Mann M, Tschöp MH, Daniel C, (2017) "A Stat6/Pten Axis Links Regulatory T Cells with Adipose Tissue Function." <i>Cell Metab</i> <b>26</b>(3):475–492.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28877454 28877454]; doi: [https://dx.doi.org/10.1016/j.cmet.2017.08.008 10.1016/j.cmet.2017.08.008]; GPMDB: [http://gpmdb.org/data/keyword/28877454 31]. | ||
- | #Chen TW, Lee CC, Liu H, Wu CS, Pickering CR, Huang PJ, Wang J, Chang IY, Yeh YM, Chen CD, Li HP, Luo JD, Tan BC, Chan TEH, Hsueh C, Chu LJ, Chen YT, Zhang B, Yang CY, Wu CC, Hsu CW, See LC, Tang P, Yu JS, Liao WC, Chiang WF, Rodriguez H, Myers JN, Chang KP, Chang YS, (2017) "APOBEC3A is an oral cancer prognostic biomarker in Taiwanese carriers of an APOBEC deletion polymorphism." <i>Nat Commun</i> <b>8</b>(1):465; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28878238 28878238]; doi: [https://dx.doi.org/10.1038/s41467-017-00493-9 10.1038/s41467-017-00493-9]; GPMDB: [http://gpmdb.org/data/keyword/28878238 | + | #Chen TW, Lee CC, Liu H, Wu CS, Pickering CR, Huang PJ, Wang J, Chang IY, Yeh YM, Chen CD, Li HP, Luo JD, Tan BC, Chan TEH, Hsueh C, Chu LJ, Chen YT, Zhang B, Yang CY, Wu CC, Hsu CW, See LC, Tang P, Yu JS, Liao WC, Chiang WF, Rodriguez H, Myers JN, Chang KP, Chang YS, (2017) "APOBEC3A is an oral cancer prognostic biomarker in Taiwanese carriers of an APOBEC deletion polymorphism." <i>Nat Commun</i> <b>8</b>(1):465; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28878238 28878238]; doi: [https://dx.doi.org/10.1038/s41467-017-00493-9 10.1038/s41467-017-00493-9]; GPMDB: [http://gpmdb.org/data/keyword/28878238 10]. |
#Han B, Fang Y, Feng M, Hu H, Hao Y, Ma C, Huo X, Meng L, Zhang X, Wu F, Li J, (2017) "Brain Membrane Proteome and Phosphoproteome Reveal Molecular Basis Associating with Nursing and Foraging Behaviors of Honeybee Workers." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28879772 28879772]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00371 10.1021/acs.jproteome.7b00371]; GPMDB: [http://gpmdb.org/data/keyword/28879772 47]. | #Han B, Fang Y, Feng M, Hu H, Hao Y, Ma C, Huo X, Meng L, Zhang X, Wu F, Li J, (2017) "Brain Membrane Proteome and Phosphoproteome Reveal Molecular Basis Associating with Nursing and Foraging Behaviors of Honeybee Workers." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28879772 28879772]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00371 10.1021/acs.jproteome.7b00371]; GPMDB: [http://gpmdb.org/data/keyword/28879772 47]. | ||
#Phillips B, Titz B, Kogel U, Sharma D, Leroy P, Xiang Y, Vuillaume G, Lebrun S, Sciuscio D, Ho J, Nury C, Guedj E, Elamin A, Esposito M, Krishnan S, Schlage WK, Veljkovic E, Ivanov NV, Martin F, Peitsch MC, Hoeng J, Vanscheeuwijck P, (2017) "Toxicity of the main electronic cigarette components, propylene glycol, glycerin, and nicotine, in Sprague-Dawley rats in a 90-day OECD inhalation study complemented by molecular endpoints." <i>Food Chem Toxicol</i> <b>109</b>(Pt 1):315–332; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28882640 28882640]; doi: [https://dx.doi.org/10.1016/j.fct.2017.09.001 10.1016/j.fct.2017.09.001]; GPMDB: [http://gpmdb.org/data/keyword/28882640 36]. | #Phillips B, Titz B, Kogel U, Sharma D, Leroy P, Xiang Y, Vuillaume G, Lebrun S, Sciuscio D, Ho J, Nury C, Guedj E, Elamin A, Esposito M, Krishnan S, Schlage WK, Veljkovic E, Ivanov NV, Martin F, Peitsch MC, Hoeng J, Vanscheeuwijck P, (2017) "Toxicity of the main electronic cigarette components, propylene glycol, glycerin, and nicotine, in Sprague-Dawley rats in a 90-day OECD inhalation study complemented by molecular endpoints." <i>Food Chem Toxicol</i> <b>109</b>(Pt 1):315–332; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28882640 28882640]; doi: [https://dx.doi.org/10.1016/j.fct.2017.09.001 10.1016/j.fct.2017.09.001]; GPMDB: [http://gpmdb.org/data/keyword/28882640 36]. | ||
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#Kollipara L, Buchkremer S, Coraspe JAG, Hathazi D, Senderek J, Weis J, Zahedi RP, Roos A, (2017) "In-depth phenotyping of lymphoblastoid cells suggests selective cellular vulnerability in Marinesco-Sjögren syndrome." <i>Oncotarget</i> <b>8</b>(40):68493–68516; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28978133 28978133]; doi: [https://dx.doi.org/10.18632/oncotarget.19663 10.18632/oncotarget.19663]; GPMDB: [http://gpmdb.org/data/keyword/28978133 23]. | #Kollipara L, Buchkremer S, Coraspe JAG, Hathazi D, Senderek J, Weis J, Zahedi RP, Roos A, (2017) "In-depth phenotyping of lymphoblastoid cells suggests selective cellular vulnerability in Marinesco-Sjögren syndrome." <i>Oncotarget</i> <b>8</b>(40):68493–68516; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28978133 28978133]; doi: [https://dx.doi.org/10.18632/oncotarget.19663 10.18632/oncotarget.19663]; GPMDB: [http://gpmdb.org/data/keyword/28978133 23]. | ||
#Opitz N, Schmitt K, Hofer-Pretz V, Neumann B, Krebber H, Braus GH, Valerius O, (2017) "Capturing the Asc1p/RACK1 microenvironment at the head region of the 40S ribosome with quantitative BioID in yeast." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28982715 28982715]; doi: [https://dx.doi.org/10.1074/mcp.M116.066654 10.1074/mcp.M116.066654]; GPMDB: [http://gpmdb.org/data/keyword/28982715 268]. | #Opitz N, Schmitt K, Hofer-Pretz V, Neumann B, Krebber H, Braus GH, Valerius O, (2017) "Capturing the Asc1p/RACK1 microenvironment at the head region of the 40S ribosome with quantitative BioID in yeast." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28982715 28982715]; doi: [https://dx.doi.org/10.1074/mcp.M116.066654 10.1074/mcp.M116.066654]; GPMDB: [http://gpmdb.org/data/keyword/28982715 268]. | ||
+ | #Parker BL, Burchfield JG, Clayton D, Geddes TA, Payne RJ, Kiens B, Wojtaszewski J, Richter EA, James DE, (2017) "Multiplexed temporal quantification of the exercise-regulated plasma peptidome." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28982716 28982716]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000020 10.1074/mcp.RA117.000020]; GPMDB: [http://gpmdb.org/data/keyword/28982716 12]. | ||
#Novikova SE, Tikhonova OV, Kurbatov LK, Farafonova TE, Vakhrushev IV, Zgoda VG, (2017) "Application of selected reaction monitoring and parallel reaction monitoring for investigation of HL-60 cell line differentiation." <i>Eur J Mass Spectrom (Chichester)</i> <b>23</b>(4):202–208; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29028392 29028392]; doi: [https://dx.doi.org/10.1177/1469066717719848 10.1177/1469066717719848]; GPMDB: [http://gpmdb.org/data/keyword/29028392 25]. | #Novikova SE, Tikhonova OV, Kurbatov LK, Farafonova TE, Vakhrushev IV, Zgoda VG, (2017) "Application of selected reaction monitoring and parallel reaction monitoring for investigation of HL-60 cell line differentiation." <i>Eur J Mass Spectrom (Chichester)</i> <b>23</b>(4):202–208; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29028392 29028392]; doi: [https://dx.doi.org/10.1177/1469066717719848 10.1177/1469066717719848]; GPMDB: [http://gpmdb.org/data/keyword/29028392 25]. | ||
#Saravanan R, Adav SS, Choong YK, van der Plas MJA, Petrlova J, Kjellström S, Sze SK, Schmidtchen A, (2017) "Proteolytic signatures define unique thrombin-derived peptides present in human wound fluid in vivo." <i>Sci Rep</i> <b>7</b>(1):13136; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29030565 29030565]; doi: [https://dx.doi.org/10.1038/s41598-017-13197-3 10.1038/s41598-017-13197-3]; GPMDB: [http://gpmdb.org/data/keyword/29030565 43]. | #Saravanan R, Adav SS, Choong YK, van der Plas MJA, Petrlova J, Kjellström S, Sze SK, Schmidtchen A, (2017) "Proteolytic signatures define unique thrombin-derived peptides present in human wound fluid in vivo." <i>Sci Rep</i> <b>7</b>(1):13136; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29030565 29030565]; doi: [https://dx.doi.org/10.1038/s41598-017-13197-3 10.1038/s41598-017-13197-3]; GPMDB: [http://gpmdb.org/data/keyword/29030565 43]. | ||
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#Chu TTT, Sinha A, Malleret B, Suwanarusk R, Park JE, Naidu R, Das R, Dutta B, Ong ST, Verma NK, Chan JK, Nosten F, Rénia L, Sze SK, Russell B, Chandramohanadas R, (2017) "Quantitative mass spectrometry of human reticulocytes reveal proteome-wide modifications during maturation." <i>Br J Haematol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29094334 29094334]; doi: [https://dx.doi.org/10.1111/bjh.14976 10.1111/bjh.14976]; GPMDB: [http://gpmdb.org/data/keyword/29094334 3]. | #Chu TTT, Sinha A, Malleret B, Suwanarusk R, Park JE, Naidu R, Das R, Dutta B, Ong ST, Verma NK, Chan JK, Nosten F, Rénia L, Sze SK, Russell B, Chandramohanadas R, (2017) "Quantitative mass spectrometry of human reticulocytes reveal proteome-wide modifications during maturation." <i>Br J Haematol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29094334 29094334]; doi: [https://dx.doi.org/10.1111/bjh.14976 10.1111/bjh.14976]; GPMDB: [http://gpmdb.org/data/keyword/29094334 3]. | ||
#Frejno M, Zenezini Chiozzi R, Wilhelm M, Koch H, Zheng R, Klaeger S, Ruprecht B, Meng C, Kramer K, Jarzab A, Heinzlmeir S, Johnstone E, Domingo E, Kerr D, Jesinghaus M, Slotta-Huspenina J, Weichert W, Knapp S, Feller SM, Kuster B, (2017) "Pharmacoproteomic characterisation of human colon and rectal cancer." <i>Mol Syst Biol</i> <b>13</b>(11):951; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29101300 29101300]; GPMDB: [http://gpmdb.org/data/keyword/29101300 184]. | #Frejno M, Zenezini Chiozzi R, Wilhelm M, Koch H, Zheng R, Klaeger S, Ruprecht B, Meng C, Kramer K, Jarzab A, Heinzlmeir S, Johnstone E, Domingo E, Kerr D, Jesinghaus M, Slotta-Huspenina J, Weichert W, Knapp S, Feller SM, Kuster B, (2017) "Pharmacoproteomic characterisation of human colon and rectal cancer." <i>Mol Syst Biol</i> <b>13</b>(11):951; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29101300 29101300]; GPMDB: [http://gpmdb.org/data/keyword/29101300 184]. | ||
+ | #Awazawa M, Gabel P, Tsaousidou E, Nolte H, Krüger M, Schmitz J, Ackermann PJ, Brandt C, Altmüller J, Motameny S, Wunderlich FT, Kornfeld JW, Blüher M, Brüning JC, (2017) "A microRNA screen reveals that elevated hepatic ectodysplasin A expression contributes to obesity-induced insulin resistance in skeletal muscle." <i>Nat Med</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29106399 29106399]; doi: [https://dx.doi.org/10.1038/nm.4420 10.1038/nm.4420]; GPMDB: [http://gpmdb.org/data/keyword/29106399 8]. | ||
#Alvarez-Castelao B, Schanzenbächer CT, Hanus C, Glock C, Tom Dieck S, Dörrbaum AR, Bartnik I, Nassim-Assir B, Ciirdaeva E, Mueller A, Dieterich DC, Tirrell DA, Langer JD, Schuman EM, (2017) "Cell-type-specific metabolic labeling of nascent proteomes in vivo." <i>Nat Biotechnol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29106408 29106408]; doi: [https://dx.doi.org/10.1038/nbt.4016 10.1038/nbt.4016]; GPMDB: [http://gpmdb.org/data/keyword/29106408 98]. | #Alvarez-Castelao B, Schanzenbächer CT, Hanus C, Glock C, Tom Dieck S, Dörrbaum AR, Bartnik I, Nassim-Assir B, Ciirdaeva E, Mueller A, Dieterich DC, Tirrell DA, Langer JD, Schuman EM, (2017) "Cell-type-specific metabolic labeling of nascent proteomes in vivo." <i>Nat Biotechnol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29106408 29106408]; doi: [https://dx.doi.org/10.1038/nbt.4016 10.1038/nbt.4016]; GPMDB: [http://gpmdb.org/data/keyword/29106408 98]. | ||
#van der Wal L, Bezstarosti K, Sap KA, Dekkers DHW, Rijkers E, Mientjes E, Elgersma Y, Demmers JAA, (2017) "Improvement of ubiquitylation site detection by Orbitrap mass spectrometry." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29122726 29122726]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.10.014 10.1016/j.jprot.2017.10.014]; GPMDB: [http://gpmdb.org/data/keyword/29122726 86]. | #van der Wal L, Bezstarosti K, Sap KA, Dekkers DHW, Rijkers E, Mientjes E, Elgersma Y, Demmers JAA, (2017) "Improvement of ubiquitylation site detection by Orbitrap mass spectrometry." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29122726 29122726]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.10.014 10.1016/j.jprot.2017.10.014]; GPMDB: [http://gpmdb.org/data/keyword/29122726 86]. | ||
+ | #Negretti NM, Gourley CR, Clair G, Adkins JN, Konkel ME, (2017) "The food-borne pathogen Campylobacter jejuni responds to the bile salt deoxycholate with countermeasures to reactive oxygen species." <i>Sci Rep</i> <b>7</b>(1):15455; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29133896 29133896]; doi: [https://dx.doi.org/10.1038/s41598-017-15379-5 10.1038/s41598-017-15379-5]; GPMDB: [http://gpmdb.org/data/keyword/29133896 8]. | ||
+ | #Doll S, Dreßen M, Geyer PE, Itzhak DN, Braun C, Doppler SA, Meier F, Deutsch MA, Lahm H, Lange R, Krane M, Mann M, (2017) "Region and cell-type resolved quantitative proteomic map of the human heart." <i>Nat Commun</i> <b>8</b>(1):1469; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29133944 29133944]; doi: [https://dx.doi.org/10.1038/s41467-017-01747-2 10.1038/s41467-017-01747-2]; GPMDB: [http://gpmdb.org/data/keyword/29133944 124]. | ||
+ | #Geis-Asteggiante L, Belew AT, Clements VK, Edwards NJ, Ostrand-Rosenberg S, El-Sayed NM, Fenselau C, (2017) "Differential content of proteins, mRNAs, and miRNAs suggests that MDSC and their exosomes may mediate distinct immune suppressive functions." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29139296 29139296]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00646 10.1021/acs.jproteome.7b00646]; GPMDB: [http://gpmdb.org/data/keyword/29139296 10]. |
GPMDB was originally constructed to serve as a reference work for all publicly available proteomics generated using tandem mass spectrometry. Public data is downloaded and reanalyzed using the current version of X! Tandem. The result files generated by the reanalysis and the relevant metadata are imported into the database and made available through the associated web site, ftp site and REST interfaces.
Contents |
The following public data repositories are checked daily for new suitable raw data for reanalysis:
Data made available from specific large projects, such as CPTAC or the Human Proteome Atlas, are also included when they are made available. Every effort is made so that reanalyzed results from all data sources are made available within 48 hours of their being released. In addition, data from lab web sites, ftp sites and direct contributions through the GPM sites made available to researchers are imported into GPMDB as part of a daily incremental update process.
GPMDB has been in operation since Jan. 1, 2004. Several large data source repositories have come into existence and ceased activity in the period since that time. All of the data from those repositories (e.g., TRANCHE, Peptidome) were reanalyzed and stored in GPMDB and they are still available even though the source repository sites are no longer active.
Simply because data is made available does not mean that it will be included in GPMDB. The data must be approved our quality control AI for its initial acceptance and it may be rejected subsequently because of either quality or originality concerns.
CAUTION: Many papers contain serious errors in their Methods sections. When using data from the literature, it is important to be skeptical of any experimental parameter (cell line, tissue type, modification reagents, quantitation methoods, etc.) that may impact on your use of the data. We have tried to correct any obvious errors, but there is no way to guarantee that we found them all. When attempting to analyze or reproduce results, keep in mind the likelyhood that even key parts of the experiment methods may have been recorded incorrectly in the associated manuscript, as methods are rarely reviewed properly in the current journal publication process.
The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of Nov. 26, 2017.