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[bioontology-support] error code 500 from about 1/2 of my annotator request

Trish Whetzel whetzel at stanford.edu
Fri Oct 1 18:50:25 PDT 2010


Thanks. I've run this data against the Annotator a few times, but have not yet reproduced the error.

Trish


On Oct 1, 2010, at 4:42 PM, Emily Howe wrote:

> I got one earlier today on this.   
> Also attached in the txt file.   
> 
> I think I can get the same data from a few more from earlier today if you need them. 
> 
> 
> The server could not fulfill the request
> http://rest.bioontology.org/obs/annotator
> {'scored': 'true', 'mappingTypes': 'null', 'format': 'tabDelimited', 'levelMax': '100', 'isVirtualOntologyId': 'True', 'textToAnnotate': '1 0 1991 11 26 2010 5 29 19 3 20 6 1 1 Homo sapiens human taxon 9606 man Homo sapiens Eukaryota; Me
> tazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo 1 2 PRI 1 19 A1BG alpha-1-B glycoprotein 19q13.4 HGNC 5 Ensembl ENSG00000121410 HPRD 00726 MIM 
> 138670 A1B ABG GAB HYST2477 DKFZp686F0970 alpha-1B-glycoprotein alpha-1B-glycoprotein The protein encoded by this gene is a plasma glycoprotein of unknown function. The protein shows sequence similarity to the variable regions of some im
> munoglobulin supergene family member proteins. [provided by RefSeq] 19q13.4 None LocusLink 1 1 1 Genome Reference Consortium Human Build 37 (GRCh37), Primary_Assembly chromosome NC_000019 9 58858171 58864864 None 224589810 3 Reference NM
> _130786 3 58858171 58858394 None 224589810 58858718 58859005 None 224589810 58861735 58862016 None 224589810 58862756 58863052 None 224589810 58863648 58863920 None 224589810 58864293 58864562 None 224589810 58864657 58864692 None 224589
> 810 58864769 58864864 None 224589810 161377438 8 Reference precursor NP_570602 2 58864769 58864802 None 224589810 58864657 58864692 None 224589810 58864293 58864562 None 224589810 58863648 58863920 None 224589810 58862756 58863052 None 2
> 24589810 58861735 58862016 None 224589810 58858718 58859005 None 224589810 58858387 58858394 None 224589810 21071030 1 Genome Reference Consortium Human Build 37 (GRCh37), Primary_Assembly scaffold NT_011109 16 31126389 31133082 None 224
> 514627 3 Reference NM_130786 3 31126389 31126612 None 224514627 31126936 31127223 None 224514627 31129953 31130234 None 224514627 31130974 31131270 None 224514627 31131866 31132138 None 224514627 31132511 31132780 None 224514627 31132875
> 31132910 None 224514627 31132987 31133082 None 224514627 161377438 8 Reference precursor NP_570602 2 31132987 31133020 None 224514627 31132875 31132910 None 224514627 31132511 31132780 None 224514627 31131866 31132138 None 224514627 311
> 30974 31131270 None 224514627 31129953 31130234 None 224514627 31126936 31127223 None 224514627 31126605 31126612 None 224514627 21071030 1 Alternate assembly (HuRef) scaffold NW_001838501 2 244990 251694 None 157812423 3 Reference NM_13
> 0786 3 244990 245085 None 157812423 245162 245197 None 157812423 245292 245561 None 157812423 245934 246206 None 157812423 246803 247099 None 157812423 247839 248120 None 157812423 250862 251149 None 157812423 251472 251694 None 15781242
> 3 161377438 8 Reference precursor NP_570602 2 245052 245085 None 157812423 245162 245197 None 157812423 245292 245561 None 157812423 245934 246206 None 157812423 246803 247099 None 157812423 247839 248120 None 157812423 250862 251149 Non
> e 157812423 251472 251479 None 157812423 21071030 1 Alternate assembly (Celera) scaffold NW_927284 1 8209443 8216141 None 89057698 3 Reference NM_130786 3 8209443 8209665 None 89057698 8209988 8210275 None 89057698 8213011 8213292 None 8
> 9057698 8214032 8214328 None 89057698 8214925 8215197 None 89057698 8215570 8215839 None 89057698 8215934 8215969 None 89057698 8216046 8216141 None 89057698 161377438 8 Reference precursor NP_570602 2 8216046 8216079 None 89057698 82159
> 34 8215969 None 89057698 8215570 8215839 None 89057698 8214925 8215197 None 89057698 8214032 8214328 None 89057698 8213011 8213292 None 89057698 8209988 8210275 None 89057698 8209658 8209665 None 89057698 21071030 1 Alternate assembly (HuRef) chromosome AC_000151 1 55167316 55174020 None 157718668 3 Reference NM_130786 3 55173925 55174020 None 157718668 55173813 55173848 None 157718668 55173449 55173718 None 157718668 55172804 55173076 None 157718668 55171911 55172207 None 157718668 55170890 55171171 None 157718668 55167861 55168148 None 157718668 55167316 55167538 None 157718668 161377438 8 Reference precursor NP_570602 2 55173925 55173958 None 157718668 55173813 55173848 None 157718668 55173449 55173718 None 157718668 55172804 55173076 None 157718668 55171911 55172207 None 157718668 55170890 55171171 None 157718668 55167861 55168148 None 157718668 55167531 55167538 None 157718668 21071030 1 Alternate assembly (Celera) chromosome AC_000062 1 55902159 55908857 None 89161197 3 Reference NM_130786 3 55902159 55902381 None 89161197 55902704 55902991 None 89161197 55905727 55906008 None 89161197 55906748 55907044 None 89161197 55907641 55907913 None 89161197 55908286 55908555 None 89161197 55908650 55908685 None 89161197 55908762 55908857 None 89161197 161377438 8 Reference precursor NP_570602 2 55908762 55908795 None 89161197 55908650 55908685 None 89161197 55908286 55908555 None 89161197 55907641 55907913 None 89161197 55906748 55907044 None 89161197 55905727 55906008 None 89161197 55902704 55902991 None 89161197 55902374 55902381 None 89161197 21071030 254 Nomenclature HUGO Gene Nomenclature Committee 16 Official Symbol A1BG 16 Official Full Name alpha-1-B glycoprotein 254 GeneOntology Provided by GOA http://www.ebi.ac.uk/GOA/ 254 Function 254 GO 3674 molecular_function evidence: ND 254 Process 254 GO 8150 biological_process evidence: ND 254 Component 254 3458201 GO 5576 extracellular region evidence: IDA 254 Mouse, Rat HomoloGene 11167 Map Viewer http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=19&MAPS=genes-r-org/rat-chr/human%3A19,genes-r-org/mouse-chr/human%3A19,genes-r-org/human-chr19&query=e%3A1[egene_id]+AND+gene[obj_type]&QSTR=a1bg&cmd=focus&fill=10 254 RefSeq Status REVIEWED 254 18706098 16335952 15489334 15461460 15221005 14760718 14702039 12477932 8889549 3610142 3458201 2591067 254 NCBI Reference Sequences (RefSeq) 254 RefSeqs maintained independently of Annotated Genomes 3 mRNA Sequence NM_130786 3 Nucleotide 161377438 NM_130786 161377438 8 Product NP_570602 2 Protein 21071030 NP_570602 alpha-1B-glycoprotein precursor 21071030 255 Conserved Domains (4) summary 255 CDD 143228 cd05751: Ig1_LILRB1_like; First immunoglobulin (Ig)-like domain found in Leukocyte Ig-like receptors (LILR)B1 (also known as LIR-1) and similar proteins 255 Location: 401 - 493 Blast Score: 330 255 CDD 176433 cl11960: Ig; Immunoglobulin domain 255 Location: 224 - 282 Blast Score: 105 255 Location: 28 - 110 Blast Score: 105 255 Location: 117 - 196 Blast Score: 91 255 Related Ensembl Ensembl ENSP00000263100 255 UniProtKB None 255 UniProtKB/Swiss-Prot P04217 P04217 255 Consensus CDS (CCDS) CCDS CCDS12976.1 CCDS12976.1 255 Source Sequence Nucleotide AB073611,AK056201,BX325198 AB073611,AK056201,BX325198 255 Related Ensembl Ensembl ENST00000263100 254 RefSeqs of Annotated Genomes: Build 37.1 1 Genome Reference Consortium Human Build 37 (GRCh37), Primary_Assembly NC_000019 9 Nucleotide 224589810 58858171 58864864 None 224589810 1 NT_011109 16 Nucleotide 224514627 31126389 31133082 None 224514627 1 Alternate assembly (Celera) AC_000062 1 Nucleotide 89161197 55902159 55908857 None 89161197 1 NW_927284 1 Nucleotide 89057698 8209443 8216141 None 89057698 1 Alternate assembly (HuRef) AC_000151 1 Nucleotide 157718668 55167316 55174020 None 157718668 1 NW_001838501 2 Nucleotide 157812423 244990 251694 None 157812423 254 Related Sequences 1 Genomic AC010642 5 Nucleotide 9929687 AC010642 41118 43580 None 9929687 8 None 1 Genomic AC012313 7 Nucleotide 21240685 AC012313 3382 11695 None 21240685 8 None 1 Genomic CH471135 1 Nucleotide 71514974 CH471135 71514974 8 EAW72575 1 Protein 119592981 EAW72575 119592981 3 mRNA AA484435 1 Nucleotide 2213248 AA484435 2213248 8 None 3 mRNA AB073611 1 Nucleotide 51555784 AB073611 51555784 8 BAD38648 1 Protein 51555785 BAD38648 51555785 3 mRNA AF414429 1 Nucleotide 15778555 AF414429 15778555 8 AAL07469 1 Protein 15778556 AAL07469 15778556 3 mRNA AI022193 1 Nucleotide 3239546 AI022193 3239546 8 None 3 mRNA AK055885 1 Nucleotide 16550723 AK055885 16550723 8 BAG51591 1 Protein 193786308 BAG51591 193786308 3 mRNA AK056201 1 Nucleotide 16551539 AK056201 16551539 8 None 3 mRNA AK289417 1 Nucleotide 158259856 AK289417 158259856 8 BAF82106 1 Protein 158259857 BAF82106 158259857 3 mRNA BC035719 1 Nucleotide 23273475 BC035719 23273475 8 AAH35719 1 Protein 23273476 AAH35719 23273476 3 mRNA BX325198 2 Nucleotide 46279733 BX325198 46279733 8 None 3 mRNA BX537419 1 Nucleotide 31873339 BX537419 31873339 8 CAD97661 1 Protein 31873340 CAD97661 31873340 3 mRNA CR603363 1 Nucleotide 50484170 CR603363 50484170 8 None 3 mRNA CR604603 1 Nucleotide 50485410 CR604603 50485410 8 None 3 mRNA CR609084 1 Nucleotide 50489891 CR609084 50489891 8 None 3 mRNA CR612720 1 Nucleotide 50493527 CR612720 50493527 8 None 3 mRNA CR614062 1 Nucleotide 50494869 CR614062 50494869 8 None 3 mRNA T80683 1 Nucleotide 703568 T80683 703568 8 None 3 mRNA W25099 1 Nucleotide 1302954 W25099 1302954 8 None 255 None 8 P04217 3 Protein 46577680 UniProtKB/Swiss-Prot P04217 46577680 8 Q7Z3U3 Protein 74713436 UniProtKB/TrEMBL Q7Z3U3 74713436 254 Additional Links 254 Evidence Viewer 1 Evidence Viewer http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=9606&contig=NT_011109.16&gene=A1BG&lid=1&from=31126389&to=31133082 254 ModelMaker 1 ModelMaker http://www.ncbi.nlm.nih.gov/mapview/modelmaker.cgi?taxid=9606&contig=NT_011109.16&from=31126389&to=31133082&gene=A1BG&lid=1 254 MIM MIM 138670 138670 254 AceView 1 AceView http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?c=geneid&org=9606&l=1 254 UCSC UCSC UCSC UCSC http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position=NM_130786 254 MGC BC035719 MGC http://mgc.nci.nih.gov/Genes/CloneList?ORG=Hs&LIST=BC035719 254 KEGG hsa:1 http://www.genome.jp/dbget-bin/www_bget?hsa:1 254 UniGene UNIGENE Hs.529161 UniGene Hs.529161 Hs.529161 http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=529161 18 MMP-9, DJ-1 and A1BG proteins are overexpressed in pancreatic juice from pancreatic ductal adenocarcinoma 18706098 2008 12 15 11 36 0 2010 1 21 0 0 0 18 A1BG-cysteine-rich secretory protein 3 complex displays a similar function in protecting the circulation from a potentially harmful effect of free CRISP-3 15461460 2007 8 25 10 2 0 2010 1 21 0 0 0 18 Interactions 18 15461460 HPRD 00726 HPRD 8 Protein 46577680 P04217 8 GeneID 10321 CRISP3 Protein 1706135 P54108 2009 12 17 15 28 0 2009 12 17 15 32 0 18 Affinity Capture-MS 15461460 BioGRID 106523 BioGRID 255 BioGRID 106523 255 GeneID 10321 CRISP3 BioGRID 115605 2007 10 7 10 5 0 2010 5 9 10 32 0 254 Markers (Sequence Tagged Sites/STS) 254 UniSTS 152074 D11S2921 (e-PCR) 255 Alternate name GDB:461809 254 UniSTS 473907 D8S2279 (e-PCR) 255 Alternate name GDB:1323207 254 UniSTS 151120 D7S2067E (e-PCR) 255 Alternate name GDB:443748 254 UniSTS 155756 D10S16 (e-PCR) 255 Alternate name D10S23 255 Alternate name GDB:193809 254 UniSTS 89991 SHGC-67307 (e-PCR) 255 Alternate name RH80032 255 Alternate name RH86145 254 UniSTS 147089 D16S325 (e-PCR) 255 Alternate name GDB:185460 254 UniSTS 10673 RH65092 (e-PCR) 255 Alternate name stSG15578 255 Alternate name WIAF-3414-STS 254 UniSTS 136670 G59506 (e-PCR) 255 Alternate name SHGC-130059 254 UniSTS 52209 WI-16009 (e-PCR) 255 Alternate name EST265925 255 Alternate name RH55926 HGNC 5 LocusID 1 MIM 138670', 'withDefaultStopWords': 'true', 'longestOnly': 'true', 'email': 'udayevani at gmail.com', 'wholeWordOnly': 'true'}
> Error code:  500
> 
> 
> 
> ________________________________________
> From: Trish Whetzel [whetzel at stanford.edu]
> Sent: Friday, October 01, 2010 4:28 PM
> To: Emily Howe
> Cc: support
> Subject: Re: [bioontology-support] error code 500 from about 1/2 of my annotator request
> 
> Hi Emily,
> 
> We were not able to verify the error. If you are still getting the 500 response, can you send the parameters you are using and example text input?
> 
> Trish
> 
> 
> On Oct 1, 2010, at 1:09 PM, Trish Whetzel wrote:
> 
>> I'll check with our Sysadmin.
>> 
>> Trish
>> 
>> 
>> On Oct 1, 2010, at 12:59 PM, Emily Howe wrote:
>> 
>>> Hi Trish,
>>> 
>>> I am trying to re-annotate some of my data.  Around 1/2 of the requests I am sending to the annotator are coming back with error code 500, internal server error.
>>> Is there a way to tell if this is an error with my data or on the server side?  Am I being throttled?
>>> 
>>> Do you have any idea?
>>> 
>>> Thanks
>>> Emily
>> 
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> 
> <500error.txt>




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