when trying to compile my bibtex file, only certain references appear and get numbered. many others however do not, and when using the bibtex command, I get an "Error – log file not found!". I have used \cite{} on all references, where some appear as a question mark even though it exists in the bib file.
Please see my .bib file
@article{cargill1999characterization,
title={Characterization of single-nucleotide polymorphisms in coding regions of human genes},
author={Cargill, Michele and Altshuler, David and Ireland, James and Sklar, Pamela and Ardlie, Kristin and Patil, Nila and Lane, Charles R and Lim, Esther P and Kalyanaraman, Nilesh and Nemesh, James and others},
journal={Nature genetics},
volume={22},
number={3},
pages={231--238},
year={1999},
publisher={Nature Publishing Group}
}
@article{collins1998dna,
title={A DNA polymorphism discovery resource for research on human genetic variation},
author={Collins, Francis S and Brooks, Lisa D and Chakravarti, Aravinda},
journal={Genome research},
volume={8},
number={12},
pages={1229--1231},
year={1998},
publisher={Cold Spring Harbor Lab}
}
@article{frazer2009human,
title={Human genetic variation and its contribution to complex traits},
author={Frazer, Kelly A and Murray, Sarah S and Schork, Nicholas J and Topol, Eric J},
journal={Nature Reviews Genetics},
volume={10},
number={4},
pages={241--251},
year={2009},
publisher={Nature Publishing Group}
}
@article{10002010map,
title={A map of human genome variation from population-scale sequencing},
author={1000 Genomes Project Consortium and others},
journal={Nature},
volume={467},
number={7319},
pages={1061--1073},
year={2010},
publisher={Nature Publishing Group}
}
@article{smigielski2000dbsnp,
title={dbSNP: a database of single nucleotide polymorphisms},
author={Smigielski, Elizabeth M and Sirotkin, Karl and Ward, Minghong and Sherry, Stephen T},
journal={Nucleic Acids Research},
volume={28},
number={1},
pages={352--355},
year={2000},
publisher={Oxford Univ Press}
}
@article{fredman2002hgvbase,
title={HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources},
author={Fredman, D and Siegfried, Marianne and Yuan, Yan P. and Bork, Peer and Lehv{\"a}slaiho, Heikki and Brookes, Anthony J},
journal={Nucleic acids research},
volume={30},
number={1},
pages={387--391},
year={2002},
publisher={Oxford Univ Press}
}
@article{hamosh2005online,
title={Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders},
author={Hamosh, Ada and Scott, Alan F and Amberger, Joanna S and Bocchini, Carol A and McKusick, Victor A},
journal={Nucleic acids research},
volume={33},
number={suppl 1},
pages={D514--D517},
year={2005},
publisher={Oxford Univ Press}
}
@article{becker2004genetic,
title={The genetic association database},
author={Becker, Kevin G and Barnes, Kathleen C and Bright, Tiffani J and Wang, S Alex},
journal={Nature genetics},
volume={36},
number={5},
pages={431--432},
year={2004},
publisher={Nature Publishing Group}
}
@article{cooper1998human,
title={The human gene mutation database},
author={Cooper, David N and Ball, Edward V and Krawczak, Michael},
journal={Nucleic acids research},
volume={26},
number={1},
pages={285--287},
year={1998},
publisher={Oxford Univ Press}
}
@article{karolchik2003ucsc,
title={The UCSC genome browser database},
author={Karolchik, Donna and Baertsch, Robert and Diekhans, Mark and Furey, Terrence S. and Hinrichs, A and Lu, YT and Roskin, Krishna M. and Schwartz, M and Sugnet, Charles W. and Thomas, Daryl J and others},
journal={Nucleic acids research},
volume={31},
number={1},
pages={51--54},
year={2003},
publisher={Oxford Univ Press}
}
@article{adzhubei2010method,
title={A method and server for predicting damaging missense mutations},
author={Adzhubei, Ivan A and Schmidt, Steffen and Peshkin, Leonid and Ramensky, Vasily E and Gerasimova, Anna and Bork, Peer and Kondrashov, Alexey S and Sunyaev, Shamil R},
journal={Nature methods},
volume={7},
number={4},
pages={248--249},
year={2010},
publisher={Nature Publishing Group}
}
@article{ng2003sift,
title={SIFT: Predicting amino acid changes that affect protein function},
author={Ng, Pauline C and Henikoff, Steven},
journal={Nucleic acids research},
volume={31},
number={13},
pages={3812--3814},
year={2003},
publisher={Oxford Univ Press}
}
@article{kumar2012evolutionary,
title={Evolutionary diagnosis method for variants in personal exomes},
author={Kumar, Sudhir and Sanderford, Maxwell and Gray, Vanessa E and Ye, Jieping and Liu, Li},
journal={Nature methods},
volume={9},
number={9},
pages={855--856},
year={2012},
publisher={Nature Publishing Group}
}
@article{hicks2011prediction,
title={Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed},
author={Hicks, Stephanie and Wheeler, David A and Plon, Sharon E and Kimmel, Marek},
journal={Human mutation},
volume={32},
number={6},
pages={661--668},
year={2011},
publisher={Wiley Online Library}
}
@article{lopes2012combined,
title={A combined functional annotation score for non-synonymous variants},
author={Lopes, Margarida C and Joyce, Chris and Ritchie, Graham RS and John, Sally L and Cunningham, Fiona and Asimit, Jennifer and Zeggini, Eleftheria},
journal={Human heredity},
volume={73},
number={1},
pages={47--51},
year={2012},
publisher={Karger Publishers}
}
@article{capriotti2011improving,
title={Improving the prediction of disease-related variants using protein three-dimensional structure},
author={Capriotti, Emidio and Altman, Russ B},
journal={BMC bioinformatics},
volume={12},
number={Suppl 4},
pages={S3},
year={2011},
publisher={BioMed Central Ltd}
}
@article{bromberg2007snap,
title={SNAP: predict effect of non-synonymous polymorphisms on function},
author={Bromberg, Yana and Rost, Burkhard},
journal={Nucleic acids research},
volume={35},
number={11},
pages={3823--3835},
year={2007},
publisher={Oxford Univ Press}
}
@article{bromberg2007snap,
title={SNAP: predict effect of non-synonymous polymorphisms on function},
author={Bromberg, Yana and Rost, Burkhard},
journal={Nucleic acids research},
volume={35},
number={11},
pages={3823--3835},
year={2007},
publisher={Oxford Univ Press}
}
@article{collins2001implications,
title={Implications of the Human Genome Project for medical science},
author={Collins, Francis S and McKusick, Victor A},
journal={Jama},
volume={285},
number={5},
pages={540--544},
year={2001},
publisher={American Medical Association}
}
@article{lyons2009sail,
title={The SAIL databank: linking multiple health and social care datasets},
author={Lyons, Ronan A and Jones, Kerina H and John, Gareth and Brooks, Caroline J and Verplancke, Jean-Philippe and Ford, David V and Brown, Ginevra and Leake, Ken},
journal={BMC Medical Informatics and Decision Making},
volume={9},
number={1},
pages={3},
year={2009},
publisher={BioMed Central Ltd}
}
@article{guttmacher2002genomic,
title={Genomic medicine—a primer},
author={Guttmacher, Alan E and Collins, Francis S and Guttmacher, Alan E and Collins, Francis S},
journal={New England Journal of Medicine},
volume={347},
number={19},
pages={1512--1520},
year={2002},
publisher={Mass Medical Soc}
}
@article{green2011charting,
title={Charting a course for genomic medicine from base pairs to bedside},
author={Green, Eric D and Guyer, Mark S and Institute, National Human Genome Research and others},
journal={Nature},
volume={470},
number={7333},
pages={204--213},
year={2011},
publisher={Nature Publishing Group}
}
@article{ginsburg2001personalized,
title={Personalized medicine: revolutionizing drug discovery and patient care},
author={Ginsburg, Geoffrey S and McCarthy, Jeanette J},
journal={TRENDS in Biotechnology},
volume={19},
number={12},
pages={491--496},
year={2001},
publisher={Elsevier}
}
@article{kho2013practical,
title={Practical challenges in integrating genomic data into the electronic health record},
author={Kho, Abel N and Rasmussen, Luke V and Connolly, John J and Peissig, Peggy L and Starren, Justin and Hakonarson, Hakon and Hayes, M Geoffrey},
journal={Genetics in Medicine},
volume={15},
number={10},
pages={772--778},
year={2013},
publisher={Nature Publishing Group}
}
@article{martin2002lntegratingfienomics,
title={lntegratingfienomics into Health Information Systems},
author={Martin-Sanchez, F and Mooio, V and Lopez-CamposI, G},
journal={Methods Inf Med},
volume={4},
pages={25--30},
year={2002}
}
@article{decode,
title={deCODE: A Genealogical Approach to Human Genetics in Iceland},
author={Jeffrey R Gulcher, Kari Stefansson},
year={2006},
publisher={Wiley}
}
@article{roden2008development,
title={Development of a large-scale de-identified DNA biobank to enable personalized medicine},
author={Roden, Dan M and Pulley, Jill M and Basford, Melissa A and Bernard, Gordon R and Clayton, Ellen W and Balser, Jeffrey R and Masys, Dan R},
journal={Clinical Pharmacology \& Therapeutics},
volume={84},
number={3},
pages={362--369},
year={2008},
publisher={Nature Publishing Group}
}
@article{kullo2010genome,
title={A genome-wide association study of red blood cell traits using the electronic medical record},
author={Kullo, Iftikhar J and Ding, Keyue and Jouni, Hayan and Smith, Carin Y and Chute, Christopher G},
journal={PLoS One},
volume={5},
number={9},
pages={e13011},
year={2010},
publisher={Public Library of Science}
}
@article{siva20081000,
title={1000 Genomes project},
author={Siva, Nayanah},
journal={Nature biotechnology},
volume={26},
number={3},
pages={256--256},
year={2008},
publisher={Nature Publishing Group}
}
@article{gibbs2003international,
title={The international HapMap project},
author={Gibbs, Richard A and Belmont, John W and Hardenbol, Paul and Willis, Thomas D and Yu, Fuli and Yang, Huanming and Ch'ang, Lan-Yang and Huang, Wei and Liu, Bin and Shen, Yan and others},
journal={Nature},
volume={426},
number={6968},
pages={789--796},
year={2003},
publisher={Nature Publishing Group}
}
@article{mailman2007ncbi,
title={The NCBI dbGaP database of genotypes and phenotypes},
author={Mailman, Matthew D and Feolo, Michael and Jin, Yumi and Kimura, Masato and Tryka, Kimberly and Bagoutdinov, Rinat and Hao, Luning and Kiang, Anne and Paschall, Justin and Phan, Lon and others},
journal={Nature genetics},
volume={39},
number={10},
pages={1181--1186},
year={2007},
publisher={Nature Publishing Group}
}
@article{meigs2007genome,
title={Genome-wide association with diabetes-related traits in the Framingham Heart Study},
author={Meigs, James B and Manning, Alisa K and Fox, Caroline S and Florez, Jose C and Liu, Chunyu and Cupples, L Adrienne and Dupuis, Jos{\'e}e},
journal={BMC medical genetics},
volume={8},
number={Suppl 1},
pages={S16},
year={2007},
publisher={BioMed Central Ltd}
}
@article{wong2012prediction,
title={Prediction of susceptibility to major depression by a model of interactions of multiple functional genetic variants and environmental factors},
author={Wong, ML and Dong, C and Andreev, V and Arcos-Burgos, M and Licinio, J},
journal={Molecular psychiatry},
volume={17},
number={6},
pages={624--633},
year={2012},
publisher={Nature Publishing Group}
}
@article{yucebacs2014prostate,
title={A prostate cancer model build by a novel SVM-ID3 hybrid feature selection method using both genotyping and phenotype data from dbGaP},
author={Y{\"u}ceba{\c{s}}, Sait Can and Son, Ye{\c{s}}im Ayd{\i}n},
journal={PloS one},
volume={9},
number={3},
pages={e91404},
year={2014},
publisher={Public Library of Science}
}
@article{cheadle1993direct,
title={Direct sequencing of the complete CFTR gene: the molecular characterisation of 99.5\% of CF chromosomes in Wales},
author={Cheadle, Jeremy P and Goodchild, Mary C and Meredith, Alison L},
journal={Human molecular genetics},
volume={2},
number={10},
pages={1551--1556},
year={1993},
publisher={Oxford Univ Press}
}
@article{lancaster1998brca1,
title={BRCA1 and BRCA2 in breast cancer families from Wales: moderate mutation frequency and two recurrent mutations in BRCA1.},
author={Lancaster, JM and Carney, ME and Gray, J and Myring, J and Gumbs, C and Sampson, J and Wheeler, D and France, E and Wiseman, R and Harper, P and others},
journal={British journal of cancer},
volume={78},
number={11},
pages={1417},
year={1998},
publisher={Nature Publishing Group}
}
@article{haralambos20121,
title={(1) Genetic testing for familial hypercholesterolaemia in wales: identification of recurrent and novel variants},
author={Haralambos, K and Whatley, S and Datta, D and McDowell, I},
journal={Atherosclerosis},
volume={223},
number={2},
pages={528},
year={2012},
publisher={Elsevier}
}
@article{liu2011dbnsfp,
title={dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions},
author={Liu, Xiaoming and Jian, Xueqiu and Boerwinkle, Eric},
journal={Human mutation},
volume={32},
number={8},
pages={894--899},
year={2011},
publisher={Wiley Online Library}
}
@article{schwarz2010mutationtaster,
title={MutationTaster evaluates disease-causing potential of sequence alterations},
author={Schwarz, Jana Marie and R{\"o}delsperger, Christian and Schuelke, Markus and Seelow, Dominik},
journal={Nature methods},
volume={7},
number={8},
pages={575--576},
year={2010},
publisher={Nature Publishing Group}
}
@article{wang2010annovar,
title={ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data},
author={Wang, Kai and Li, Mingyao and Hakonarson, Hakon},
journal={Nucleic acids research},
volume={38},
number={16},
pages={e164--e164},
year={2010},
publisher={Oxford Univ Press}
}
@article{altschul1997gapped,
title={Gapped BLAST and PSI-BLAST: a new generation of protein database search programs},
author={Altschul, Stephen F and Madden, Thomas L and Sch{\"a}ffer, Alejandro A and Zhang, Jinghui and Zhang, Zheng and Miller, Webb and Lipman, David J},
journal={Nucleic acids research},
volume={25},
number={17},
pages={3389--3402},
year={1997},
publisher={Oxford Univ Press}
}
@article{joosten2011series,
title={A series of PDB related databases for everyday needs},
author={Joosten, Robbie P and Te Beek, Tim AH and Krieger, Elmar and Hekkelman, Maarten L and Hooft, Rob WW and Schneider, Reinhard and Sander, Chris and Vriend, Gert},
journal={Nucleic acids research},
volume={39},
number={suppl 1},
pages={D411--D419},
year={2011},
publisher={Oxford Univ Press}
}
@article{berman2000protein,
title={The protein data bank},
author={Berman, Helen M and Westbrook, John and Feng, Zukang and Gilliland, Gary and Bhat, TN and Weissig, Helge and Shindyalov, Ilya N and Bourne, Philip E},
journal={Nucleic acids research},
volume={28},
number={1},
pages={235--242},
year={2000},
publisher={Oxford Univ Press}
}
@article{chapman2000biopython,
title={Biopython: Python tools for computational biology},
author={Chapman, Brad and Chang, Jeffrey},
journal={ACM SIGBIO Newsletter},
volume={20},
number={2},
pages={15--19},
year={2000},
publisher={ACM}
}
@article{pickrell2014epilepsy,
title={EPILEPSY PREVALENCE, INCIDENCE AND SOCIOECONOMIC DEPRIVATION},
author={Pickrell, Owen and Lacey, Arron and Bodger, Owen and Demmler, Joanne and Thomas, Rhys and Lyons, Ronan and Smith, Phil and Rees, Mark and Kerr, Mike},
journal={Journal of Neurology, Neurosurgery \& Psychiatry},
volume={85},
number={10},
pages={e4--e4},
year={2014},
publisher={BMJ Publishing Group Ltd}
}
@article{pickrell2014trends,
title={Trends in the first antiepileptic drug prescribed for epilepsy between 2000 and 2010},
author={Pickrell, W Owen and Lacey, Arron S and Thomas, Rhys H and Lyons, Ronan A and Smith, Phil EM and Rees, Mark I},
journal={Seizure},
volume={23},
number={1},
pages={77--80},
year={2014},
publisher={Elsevier}
}
@article{pickrell2012weight,
title={Weight change associated with antiepileptic drugs},
author={Pickrell, William Owen and Lacey, Arron S and Thomas, Rhys H and Smith, Philip EM and Rees, Mark I},
journal={Journal of Neurology, Neurosurgery \& Psychiatry},
pages={jnnp--2012},
year={2012},
publisher={BMJ Publishing Group Ltd}
}
can anyone see anything wrong? as I said, some references do work (altschul1997gapped) for instance.
Best Answer
I cannot replicate the error you report getting. I did notice, though, quite a few issues in your bibliography file that ought to be fixed.
Most importantly, in the
titlefields, you need to take care not to let BibTeX lowercase words that should not be lowercased. Among them are words such asWales(the country) and acrynonyms (DNA,HGVbase).Some authors are "Corporate Authors", e.g.,
If you take no care, the first author will be interpreted by BibTeX as having given names "1000", "Genomes", and "Project" and surname "Consortium" (and thus be sorted under C for Consortium!). Yikes!! You need to write this author field as
ie., encase the entire first author's name in an extra pair of curly braces. Similarly, you need to write
Take care to use only the keyword
andbut no commas to separate authors. In the entry with keydecode, you currently haveBy BibTeX's syntax rules, this entry will be interpreted as having a single author with a triple-word last name ("Jeffrey R Gulcher") and two first names -- "Kari" and "Stefansson"; it will thus also be sorted under "J" for "Jeffrey" rather than under "G" for "Gulcher". I believe this field should be
You're doing a very good job inputting accented characters, but there are some other non-7bit-ASCII characters present in the bib bile. E.g., you need to replace
—with---to get an em-dash.No point in having duplicate entries, right? Hence, do delete the second instance of the entry with key bromberg2007snap".
Optional (and not implemented in the code below): I would also add periods ("full stops") at the ends of abbreviated given names, i.e., write
Collins, Francis S. and Brooks, Lisa D.instead ofCollins, Francis S and Brooks, Lisa D. If the bibliography style you use happens to delete the periods, that's fine. However, no bib style file I know of will add the periods automatically if they're missing.Somewhere between optional and required, but certainly quite desirable (and also not implemented in the code below): You should try to keep the information about the authors' names consistent across entries. E.g., you have the following two entries:
The latter entry provides middle initials for all authors, whereas the former does not. Just to avoid any confusion about whether these authors are the same, you should provide the missing pieces of information in the former entry.