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Items: 40

1.

FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration.

Dooley DM, Griffiths EJ, Gosal GS, Buttigieg PL, Hoehndorf R, Lange MC, Schriml LM, Brinkman FSL, Hsiao WWL.

NPJ Sci Food. 2018 Dec 18;2:23. doi: 10.1038/s41538-018-0032-6. eCollection 2018.

2.

Consent insufficient for data release-Response.

Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I.

Science. 2019 May 3;364(6439):446. doi: 10.1126/science.aax7509. No abstract available.

PMID:
31048484
3.

Toward unrestricted use of public genomic data.

Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I.

Science. 2019 Jan 25;363(6425):350-352. doi: 10.1126/science.aaw1280. No abstract available.

4.

ECO, the Evidence & Conclusion Ontology: community standard for evidence information.

Giglio M, Tauber R, Nadendla S, Munro J, Olley D, Ball S, Mitraka E, Schriml LM, Gaudet P, Hobbs ET, Erill I, Siegele DA, Hu JC, Mungall C, Chibucos MC.

Nucleic Acids Res. 2019 Jan 8;47(D1):D1186-D1194. doi: 10.1093/nar/gky1036.

5.

Human Disease Ontology 2018 update: classification, content and workflow expansion.

Schriml LM, Mitraka E, Munro J, Tauber B, Schor M, Nickle L, Felix V, Jeng L, Bearer C, Lichenstein R, Bisordi K, Campion N, Hyman B, Kurland D, Oates CP, Kibbey S, Sreekumar P, Le C, Giglio M, Greene C.

Nucleic Acids Res. 2019 Jan 8;47(D1):D955-D962. doi: 10.1093/nar/gky1032.

6.

Disease Ontology: improving and unifying disease annotations across species.

Bello SM, Shimoyama M, Mitraka E, Laulederkind SJF, Smith CL, Eppig JT, Schriml LM.

Dis Model Mech. 2018 Mar 12;11(3). pii: dmm032839. doi: 10.1242/dmm.032839.

7.

Molecular, phenotypic, and sample-associated data to describe pluripotent stem cell lines and derivatives.

Daily K, Ho Sui SJ, Schriml LM, Dexheimer PJ, Salomonis N, Schroll R, Bush S, Keddache M, Mayhew C, Lotia S, Perumal TM, Dang K, Pantano L, Pico AR, Grassman E, Nordling D, Hide W, Hatzopoulos AK, Malik P, Cancelas JA, Lutzko C, Aronow BJ, Omberg L.

Sci Data. 2017 Mar 28;4:170030. doi: 10.1038/sdata.2017.30.

8.

The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.

Groza T, Köhler S, Moldenhauer D, Vasilevsky N, Baynam G, Zemojtel T, Schriml LM, Kibbe WA, Schofield PN, Beck T, Vasant D, Brookes AJ, Zankl A, Washington NL, Mungall CJ, Lewis SE, Haendel MA, Parkinson H, Robinson PN.

Am J Hum Genet. 2015 Jul 2;97(1):111-24. doi: 10.1016/j.ajhg.2015.05.020. Epub 2015 Jun 25.

9.

The Disease Ontology: fostering interoperability between biological and clinical human disease-related data.

Schriml LM, Mitraka E.

Mamm Genome. 2015 Oct;26(9-10):584-9. doi: 10.1007/s00335-015-9576-9. Epub 2015 Jun 21.

10.

Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis.

Wu TJ, Schriml LM, Chen QR, Colbert M, Crichton DJ, Finney R, Hu Y, Kibbe WA, Kincaid H, Meerzaman D, Mitraka E, Pan Y, Smith KM, Srivastava S, Ward S, Yan C, Mazumder R.

Database (Oxford). 2015 Apr 4;2015:bav032. doi: 10.1093/database/bav032. Print 2015.

11.

Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data.

Kibbe WA, Arze C, Felix V, Mitraka E, Bolton E, Fu G, Mungall CJ, Binder JX, Malone J, Vasant D, Parkinson H, Schriml LM.

Nucleic Acids Res. 2015 Jan;43(Database issue):D1071-8. doi: 10.1093/nar/gku1011. Epub 2014 Oct 27.

12.

Standardized metadata for human pathogen/vector genomic sequences.

Dugan VG, Emrich SJ, Giraldo-Calderón GI, Harb OS, Newman RM, Pickett BE, Schriml LM, Stockwell TB, Stoeckert CJ Jr, Sullivan DE, Singh I, Ward DV, Yao A, Zheng J, Barrett T, Birren B, Brinkac L, Bruno VM, Caler E, Chapman S, Collins FH, Cuomo CA, Di Francesco V, Durkin S, Eppinger M, Feldgarden M, Fraser C, Fricke WF, Giovanni M, Henn MR, Hine E, Hotopp JD, Karsch-Mizrachi I, Kissinger JC, Lee EM, Mathur P, Mongodin EF, Murphy CI, Myers G, Neafsey DE, Nelson KE, Nierman WC, Puzak J, Rasko D, Roos DS, Sadzewicz L, Silva JC, Sobral B, Squires RB, Stevens RL, Tallon L, Tettelin H, Wentworth D, White O, Will R, Wortman J, Zhang Y, Scheuermann RH.

PLoS One. 2014 Jun 17;9(6):e99979. doi: 10.1371/journal.pone.0099979. eCollection 2014.

13.

MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment.

Glass EM, Dribinsky Y, Yilmaz P, Levin H, Van Pelt R, Wendel D, Wilke A, Eisen JA, Huse S, Shipanova A, Sogin M, Stajich J, Knight R, Meyer F, Schriml LM.

ISME J. 2014 Jan;8(1):1-3. doi: 10.1038/ismej.2013.176. Epub 2013 Oct 24. No abstract available.

14.

Report of the 13(th) Genomic Standards Consortium Meeting, Shenzhen, China, March 4-7, 2012.

Gilbert JA, Bao Y, Wang H, Sansone SA, Edmunds SC, Morrison N, Meyer F, Schriml LM, Davies N, Sterk P, Wilkening J, Garrity GM, Field D, Robbins R, Smith DP, Mizrachi I, Moreau C.

Stand Genomic Sci. 2012 May 25;6(2):276-86. doi: 10.4056/sigs.2876184. Epub 2012 May 4.

15.

Disease Ontology: a backbone for disease semantic integration.

Schriml LM, Arze C, Nadendla S, Chang YW, Mazaitis M, Felix V, Feng G, Kibbe WA.

Nucleic Acids Res. 2012 Jan;40(Database issue):D940-6. doi: 10.1093/nar/gkr972. Epub 2011 Nov 12.

16.

The Genomic Standards Consortium.

Field D, Amaral-Zettler L, Cochrane G, Cole JR, Dawyndt P, Garrity GM, Gilbert J, Glöckner FO, Hirschman L, Karsch-Mizrachi I, Klenk HP, Knight R, Kottmann R, Kyrpides N, Meyer F, San Gil I, Sansone SA, Schriml LM, Sterk P, Tatusova T, Ussery DW, White O, Wooley J.

PLoS Biol. 2011 Jun;9(6):e1001088. doi: 10.1371/journal.pbio.1001088. Epub 2011 Jun 21.

17.

Metagenomics: A foundling finds its feet.

Gilbert JA, Meyer F, Field D, Schriml LM, Garrity GM.

Stand Genomic Sci. 2010 Oct 27;3(2):212-3. doi: 10.4056/sigs.1213842. No abstract available.

18.

GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database.

Schriml LM, Arze C, Nadendla S, Ganapathy A, Felix V, Mahurkar A, Phillippy K, Gussman A, Angiuoli S, Ghedin E, White O, Hall N.

Nucleic Acids Res. 2010 Jan;38(Database issue):D754-64. doi: 10.1093/nar/gkp832. Epub 2009 Oct 22.

19.

Laying the foundation for a Genomic Rosetta Stone: creating information hubs through the use of consensus identifiers.

Van Brabant B, Gray T, Verslyppe B, Kyrpides N, Dietrich K, Glöckner FO, Cole J, Farris R, Schriml LM, De Vos P, De Baets B, Field D, Dawyndt P; Genomic Standards Consortium.

OMICS. 2008 Jun;12(2):123-7. doi: 10.1089/omi.2008.0020.

PMID:
18479205
20.

Habitat-Lite: a GSC case study based on free text terms for environmental metadata.

Hirschman L, Clark C, Cohen KB, Mardis S, Luciano J, Kottmann R, Cole J, Markowitz V, Kyrpides N, Morrison N, Schriml LM, Field D; Novo Project.

OMICS. 2008 Jun;12(2):129-36. doi: 10.1089/omi.2008.0016.

PMID:
18416669
21.

Resources for genetic and genomic studies of Xenopus.

Klein SL, Gerhard DS, Wagner L, Richardson P, Schriml LM, Sater AK, Warren WC, McPherson JD.

Methods Mol Biol. 2006;322:1-16. Review.

PMID:
16739712
22.

Database resources of the National Center for Biotechnology Information.

Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Geer LY, Helmberg W, Kapustin Y, Kenton DL, Khovayko O, Lipman DJ, Madden TL, Maglott DR, Ostell J, Pruitt KD, Schuler GD, Schriml LM, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Suzek TO, Tatusov R, Tatusova TA, Wagner L, Yaschenko E.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D173-80.

23.

Database resources of the National Center for Biotechnology Information.

Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Church DM, DiCuccio M, Edgar R, Federhen S, Helmberg W, Kenton DL, Khovayko O, Lipman DJ, Madden TL, Maglott DR, Ostell J, Pontius JU, Pruitt KD, Schuler GD, Schriml LM, Sequeira E, Sherry ST, Sirotkin K, Starchenko G, Suzek TO, Tatusov R, Tatusova TA, Wagner L, Yaschenko E.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D39-45.

24.

Database resources of the National Center for Biotechnology Information: update.

Wheeler DL, Church DM, Edgar R, Federhen S, Helmberg W, Madden TL, Pontius JU, Schuler GD, Schriml LM, Sequeira E, Suzek TO, Tatusova TA, Wagner L.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D35-40.

25.

Development and evaluation of an automated annotation pipeline and cDNA annotation system.

Kasukawa T, Furuno M, Nikaido I, Bono H, Hume DA, Bult C, Hill DP, Baldarelli R, Gough J, Kanapin A, Matsuda H, Schriml LM, Hayashizaki Y, Okazaki Y, Quackenbush J.

Genome Res. 2003 Jun;13(6B):1542-51.

26.

Connecting sequence and biology in the laboratory mouse.

Baldarelli RM, Hill DP, Blake JA, Adachi J, Furuno M, Bradt D, Corbani LE, Cousins S, Frazer KS, Qi D, Yang L, Ramachandran S, Reed D, Zhu Y, Kasukawa T, Ringwald M, King BL, Maltais LJ, McKenzie LM, Schriml LM, Maglott D, Church DM, Pruitt K, Eppig JT, Richardson JE, Kadin JA, Bult CJ.

Genome Res. 2003 Jun;13(6B):1505-19.

27.

Human disease genes and their cloned mouse orthologs: exploration of the FANTOM2 cDNA sequence data set.

Schriml LM, Hill DP, Blake JA, Bono H, Wynshaw-Boris A, Pavan WJ, Ring BZ, Beisel K, Setou M, Okazaki Y; RIKEN GER Group; GSL Members.

Genome Res. 2003 Jun;13(6B):1496-500.

28.

Database resources of the National Center for Biotechnology.

Wheeler DL, Church DM, Federhen S, Lash AE, Madden TL, Pontius JU, Schuler GD, Schriml LM, Sequeira E, Tatusova TA, Wagner L.

Nucleic Acids Res. 2003 Jan 1;31(1):28-33.

29.

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.

Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, Nogami A, Schönbach C, Gojobori T, Baldarelli R, Hill DP, Bult C, Hume DA, Quackenbush J, Schriml LM, Kanapin A, Matsuda H, Batalov S, Beisel KW, Blake JA, Bradt D, Brusic V, Chothia C, Corbani LE, Cousins S, Dalla E, Dragani TA, Fletcher CF, Forrest A, Frazer KS, Gaasterland T, Gariboldi M, Gissi C, Godzik A, Gough J, Grimmond S, Gustincich S, Hirokawa N, Jackson IJ, Jarvis ED, Kanai A, Kawaji H, Kawasawa Y, Kedzierski RM, King BL, Konagaya A, Kurochkin IV, Lee Y, Lenhard B, Lyons PA, Maglott DR, Maltais L, Marchionni L, McKenzie L, Miki H, Nagashima T, Numata K, Okido T, Pavan WJ, Pertea G, Pesole G, Petrovsky N, Pillai R, Pontius JU, Qi D, Ramachandran S, Ravasi T, Reed JC, Reed DJ, Reid J, Ring BZ, Ringwald M, Sandelin A, Schneider C, Semple CA, Setou M, Shimada K, Sultana R, Takenaka Y, Taylor MS, Teasdale RD, Tomita M, Verardo R, Wagner L, Wahlestedt C, Wang Y, Watanabe Y, Wells C, Wilming LG, Wynshaw-Boris A, Yanagisawa M, Yang I, Yang L, Yuan Z, Zavolan M, Zhu Y, Zimmer A, Carninci P, Hayatsu N, Hirozane-Kishikawa T, Konno H, Nakamura M, Sakazume N, Sato K, Shiraki T, Waki K, Kawai J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Imotani K, Ishii Y, Itoh M, Kagawa I, Miyazaki A, Sakai K, Sasaki D, Shibata K, Shinagawa A, Yasunishi A, Yoshino M, Waterston R, Lander ES, Rogers J, Birney E, Hayashizaki Y; FANTOM Consortium; RIKEN Genome Exploration Research Group Phase I & II Team.

Nature. 2002 Dec 5;420(6915):563-73.

PMID:
12466851
30.

Database resources of the National Center for Biotechnology Information: 2002 update.

Wheeler DL, Church DM, Lash AE, Leipe DD, Madden TL, Pontius JU, Schuler GD, Schriml LM, Tatusova TA, Wagner L, Rapp BA.

Nucleic Acids Res. 2002 Jan 1;30(1):13-6.

31.

Comparative analysis of the promoter structure and genomic organization of the human and mouse ABCA7 gene encoding a novel ABCA transporter.

Broccardo C, Osorio J, Luciani MF, Schriml LM, Prades C, Shulenin S, Arnould I, Naudin L, Lafargue C, Rosier M, Jordan B, Mattei MG, Dean M, Denèfle P, Chimini G.

Cytogenet Cell Genet. 2001;92(3-4):264-70.

PMID:
11435699
32.

An ATP-binding cassette gene (ABCG5) from the ABCG (White) gene subfamily maps to human chromosome 2p21 in the region of the Sitosterolemia locus.

Shulenin S, Schriml LM, Remaley AT, Fojo S, Brewer B, Allikmets R, Dean M.

Cytogenet Cell Genet. 2001;92(3-4):204-8.

PMID:
11435688
33.

Functional annotation of a full-length mouse cDNA collection.

Kawai J, Shinagawa A, Shibata K, Yoshino M, Itoh M, Ishii Y, Arakawa T, Hara A, Fukunishi Y, Konno H, Adachi J, Fukuda S, Aizawa K, Izawa M, Nishi K, Kiyosawa H, Kondo S, Yamanaka I, Saito T, Okazaki Y, Gojobori T, Bono H, Kasukawa T, Saito R, Kadota K, Matsuda H, Ashburner M, Batalov S, Casavant T, Fleischmann W, Gaasterland T, Gissi C, King B, Kochiwa H, Kuehl P, Lewis S, Matsuo Y, Nikaido I, Pesole G, Quackenbush J, Schriml LM, Staubli F, Suzuki R, Tomita M, Wagner L, Washio T, Sakai K, Okido T, Furuno M, Aono H, Baldarelli R, Barsh G, Blake J, Boffelli D, Bojunga N, Carninci P, de Bonaldo MF, Brownstein MJ, Bult C, Fletcher C, Fujita M, Gariboldi M, Gustincich S, Hill D, Hofmann M, Hume DA, Kamiya M, Lee NH, Lyons P, Marchionni L, Mashima J, Mazzarelli J, Mombaerts P, Nordone P, Ring B, Ringwald M, Rodriguez I, Sakamoto N, Sasaki H, Sato K, Schönbach C, Seya T, Shibata Y, Storch KF, Suzuki H, Toyo-oka K, Wang KH, Weitz C, Whittaker C, Wilming L, Wynshaw-Boris A, Yoshida K, Hasegawa Y, Kawaji H, Kohtsuki S, Hayashizaki Y; RIKEN Genome Exploration Research Group Phase II Team and the FANTOM Consortium.

Nature. 2001 Feb 8;409(6821):685-90.

PMID:
11217851
34.

An ATP-binding cassette gene (ABCG3) closely related to the multidrug transporter ABCG2 (MXR/ABCP) has an unusual ATP-binding domain.

Mickley L, Jain P, Miyake K, Schriml LM, Rao K, Fojo T, Bates S, Dean M.

Mamm Genome. 2001 Jan;12(1):86-8. No abstract available.

PMID:
11178751
35.

Use of denaturing HPLC to map human and murine genes and to validate single-nucleotide polymorphisms.

Schriml LM, Peterson RJ, Gerrard B, Dean M.

Biotechniques. 2000 Apr;28(4):740-5.

36.
37.

Database resources of the National Center for Biotechnology Information.

Wheeler DL, Church DM, Lash AE, Leipe DD, Madden TL, Pontius JU, Schuler GD, Schriml LM, Tatusova TA, Wagner L, Rapp BA.

Nucleic Acids Res. 2001 Jan 1;29(1):11-6.

38.

Mutational spectra of PTEN/MMAC1 gene: a tumor suppressor with lipid phosphatase activity.

Ali IU, Schriml LM, Dean M.

J Natl Cancer Inst. 1999 Nov 17;91(22):1922-32. Review.

PMID:
10564676
39.

Tyramide signal amplification (TSA)-FISH applied to mapping PCR-labeled probes less than 1 kb in size.

Schriml LM, Padilla-Nash HM, Coleman A, Moen P, Nash WG, Menninger J, Jones G, Ried T, Dean M.

Biotechniques. 1999 Sep;27(3):608-13.

40.

A human placenta-specific ATP-binding cassette gene (ABCP) on chromosome 4q22 that is involved in multidrug resistance.

Allikmets R, Schriml LM, Hutchinson A, Romano-Spica V, Dean M.

Cancer Res. 1998 Dec 1;58(23):5337-9.

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