2010年度 DDBJ事業報告e

=DDBJ release making and construction of international base sequence data base (INSD) =


 * DDBJ composes international base sequence data base (International Nucleotide Sequence Database Collaboration; INSDC) with Britain EMBL and United States GenBank.
 * A university all over the world and the researcher of the enterprise make "DNA sequence information" public along with thesis submission and the patent application, etc.
 * Looking for something is difficult when disjointedly recording in Patent Office in a lot of magazine houses and a lot of countries.
 * INSDC does help that makes the common fortune by which the collect everyone can use the DNA sequence and the explanation for one place by the whole society's cooperating in the same type.
 * It grew up in the world cooperation business that another did not have the example in 25 years by having decided it to obligating registration to INSDC in a lot of magazine editors' cooperation, and the use of the Patent Office cooperation of INSDC.
 * INSDC makes three organizations in three areas and the registration vote archive of three copies that each other is exchanged respectively as an equal entrance and information after like the link information etc. is slightly different is made.
 * These three copy data is called DDBJ, GenBank, and EMBL.
 * 100 million array registration votes or more are made up to now repeat this work for 25 years.
 * It becomes possible the retrieval inspection and to take all over the world within one day after the date of opening to the public the array registration vote brought together.
 * Moreover, three organizations write down the array of 12 from 4 all registration vote every year and make huge text file "Release file".
 * The information addition is freely done in each organization, and in this case, EMBL, GenBank, and DDBJ can be released.
 * I will .. W-DDBJ, Registration accepted with DDBJ, and J-DDBJ .. call the copy of the DDBJ style of all INSDC data as an internal jargon only of this report.
 * Release is taken secondarily of another organization and corporate DB and used for the data update.
 * Moreover, release is used for the research material of the evolution study, genetics, the medicine, and [baioinfomatei;kku].

Registration action Submission level breakdown of W-DDBJ release (Registration of the unopening to the public is not included) to all INSDC

 * The transition of the science was undertaken and the array registration vote changed from "It was written to know and added the array" attitude into the attitude of "The array feature of the object of the uncertainty is this", too.
 * The transition like the above-mentioned is undertaken, the best shape to register the array vote is diversified, too and divisions such as EST, WGS, and GSS have come into existence. Moreover, the registration of the raw data before bringing it together in the array vote arises, too.
 * It is a value made a cluster by the document and author information etc. on the registration vote to express not the number of array registration votes but the number of bases and the frequency of the registration action. Making the array registration vote included in release a cluster uses the bank contents data that was entrusted from the integrated data base business and developed since 2007.
 * Data that made DDBJ release (the 1st) data INSDC contents (the 2nd) at the integrated data base center was analyzed again. *Each column is [fun] no supplementation (mutually exclusive) to each other.
 *  open to the publicfrom January 1 in each fiscal year to December 31 is totaled for the convenience of statistics. Unpublished registration is not included though it was accepted. [Yasushitsukasado] contents integration data base center re-analysis Watanabe (Takagi task force TTF) Tamotsu Ohisa

DDBJへの登録行為 Submission level breakdown of J-DDBJ(未公開の登録は含まず）

 * The registration frequency corresponds to the registration frequency to Patent Office because the registration of patent is brought together once in Patent Office.

International practitioner conference (ICM) and advisory committee

 * The person in charge of GenBank, EMBL, and DDBJ gathers to report, to discuss, and to unite new correspondence to data and the correction of the description rule, etc. at the ordinary year and the international practitioner conference (International Collaborative Meeting and ICM; practitioner conference) is held by carrying about.

< EVENT> 23rd ICM  2010-5-19/2010-5-21: British [hinkusuton] < ATTENDANT> Nakamura and Y.; Mashima,J.; Kodama,Y.  reflected in FT-doc xx. < EVENT> 22nd ICM  2009-5-12/2009-5-15: United States Bethesda < ATTENDANT> Okubo and K.; Nakamura,Y.; Tateno,Y.; Mashima,J.; Kodama,Y. < EVENT> 19th ICM  2006-5-15/2006-5-17: United States Bethesda < ATTENDANT> Tateno and Y.; Sugawara,H.; Mashima,J.; Okido,T. < EVENT> 16th ICM  2003-5-19/2003-5-21: United States Bethesda < ATTENDANT> Tateno and Y.; Sugawara,H.; Miyazaki,S.; Mashima,J.; Sakai,K. < ATTENDANT> all_DDBJ
 * Sugawara,H.; Saitou,N.; Ikeo,K.; Suzuki,Y.; Mashima,J.; Aono,H.
 * Sugawara,H.; Fukuchi,S.; Mashima,J.; Kosuge,T.

< EVENT> 15th ICM  2002-5-20/2002-5-22: Shizuoka Prefecture Mishima city

 20th IAC  2009-07-01  international videoconferencing (Japan: National informatics laboratory) Satoru < ATTENDANT > Miyano (The University of Tokyo Institute of Medical Science) and Kan'no pure husband (The University of Tokyo graduate school) < OBSERVER> Gojobori and T.; Okubo,K.; Nakamura,Y. < EVENT> 19th IAC  2008-08-22  international videoconferencing (Japan: National informatics laboratory) [akiotto] < ATTENDANT > Fujiyama (national informatics laboratory), Kan'no pure husband (The University of Tokyo graduate school), and Haruki Nakamura (Osaka University) < OBSERVER> Gojobori and T.; Sugawara,H.; Tateno,Y.; Ikeo,K. < EVENT> 18th IAC <DATE> 2007-06-19 <PLACE > international videoconferencing (Japan: National informatics laboratory) [akiotto] < ATTENDANT > Fujiyama (national informatics laboratory), Kan'no pure husband (The University of Tokyo graduate school), and Haruki Nakamura (Osaka University) < OBSERVER> Gojobori and T.; Sugawara,H.; Tateno,Y.; Saitou,N.; Ikeo,K. [Akiotto] < EVENT> 17th IAC <DATE> 2006-05-18 <PLACE > United States Bethesda < ATTENDANT > Fujiyama (national informatics laboratory), Kan'no pure husband (The University of Tokyo graduate school), and Haruki Nakamura (Osaka University) < OBSERVER> Gojobori and T.; Sugawara,H.; Tateno,Y.; Saitou,N.; Okubo,K.; Ikeo,K. Kenichi < EVENT> 16th IAC <DATE> 2005-05-19/2005-05-20 <PLACE > Shizuoka Prefecture Mishima city < ATTENDANT > Matsubara (gene chip laboratory Ltd.), [akiotto] Fujiyama (national informatics laboratory), and Kan'no pure husband (The University of Tokyo graduate school) < OBSERVER> Gojobori, T.; Sugawara, H.; Tateno, Y.; Saitou, N.; Okubo, and K. [Akiotto] < EVENT> 15th IAC <DATE> 2004-05-20/2004-05-21 <PLACE > Britain [hinkusuton] < ATTENDANT > Fujiyama (national informatics laboratory) and Haruki Nakamura (Osaka University) < OBSERVER> Gojobori and T.; Sugawara,H.; Tateno,Y.; Okubo,K.; Fukuchi,S.
 * International advisory committee (International Advisory Committee, IAC) is a conference to consult the representative in the region of research about the matter with an important bank business.

General registration receipt

 * The registration of the new base sequence text with the explanation from the personal author can be the following three methods and be the acceptances.
 * Each method is registered in the data base of DDBJ after data bank construction team's (15 people and tables below) assessments are passed, and is open to the public at the release date that the enrollee directed.

1. Registration SAKURA by Web form
charge [anote-tarisuto] Mayumi Britain Dr. Takeshi of Dr. Atsushi Mashima (science) living thing physicochemical major Kosuga (science) biotechnology major Aono hero Tsutsui wave [**] inlet Shima
 * Please complete one array registration vote by filling it in on the Web form according to the inducement.
 * It is written in DDBJ acceptance RDB HiR-DDBJ.
 * The description leakage and irrationality question the registered form content by mail if the person in charge whether checks, and there is an uncertainty the day before every morning and it ..filling in.. is concluded.

2. Batch registration in individual window (Mass Submission System; MSS)
charge [anote-tarisuto] [Han] doctor (agriculture) application life chemistry major Nozaki sub-[**] beauty Yokoyama association beauty </ ..delighting.. pre of Dr. [korihisashi] Oshiro (agriculture) gene resource engineering major Lee >
 * The contact doing and the person in charge individually exchange by mail in the address for the acceptance and it encourages it.
 * It looks for the data of the registration hope and the registration category is classified.
 * Please fill in a common meta data part to two or more registration votes on the Excel template.
 * A peculiar array part to the array vote is prepared by the Fasta form and gotten by me in the prepared account.
 * After the person in charge checks the put file, it turns it on to HiR-DDBJ.

4. Five years at registration history bygone to DDBJ
All the registration that DDBJ had accepted for the past five years was totaled according to the registration method. A black felt-tipped marker does and is included as for registration that is the unopening to the public now.

<DDBJstat>SubmissionSAKURA<Period>2006-01-01/2006-12-31<Occurrence>3819<Note>records submitted=22525; OPENEDat2011-03=96.9% <DDBJstat>SubmissionSAKURA<Period>2007-01-01/2007-12-31<Occurrence>3935<Note>records submitted=21296; OPENEDat2011-03=92.4% <DDBJstat>SubmissionSAKURA<Period>2008-01-01/2008-12-31<Occurrence>3623<Note>records submitted=25406; OPENEDat2011-03=95.8% <DDBJstat>SubmissionSAKURA<Period>2009-01-01/2009-12-31<Occurrence>3976<Note>records submitted=28357; OPENEDat2011-03=87.9% <DDBJstat>SubmissionMASS<Period>2006-01-01/2006-12-31<Occurrence>284<Note>records submitted=3052461; OPENEDat2011-03=91.2% <DDBJstat>SubmissionMASS<Period>2007-01-01/2007-12-31<Occurrence>328<Note>records submitted=2928840; OPENEDat2011-03=92.7% <DDBJstat>SubmissionMASS<Period>2008-01-01/2008-12-31<Occurrence>312<Note>records submitted=1578373; OPENEDat2011-03=92.6% <DDBJstat>SubmissionMASS<Period>2009-01-01/2009-12-31<Occurrence>315<Note>records submitted=1735029; OPENEDat2011-03=82.2% <DDBJstat>SubmissionMASS<Period>2010-01-01/2010-12-31<Occurrence>305<Note>records submitted=1901302; OPENEDat2011-03=50.5%

The data base log that becomes the origin of the total above is taken out and it underlays. Sensitive information in the part of the unopening to the public is a black felt-tipped marker settlement.

"Head-100" of the 2010 file shown below


 * For instance, the first line is read, "It is SAKURA, plant DNA of one 688nt is registered on January 4 of 2010, and opened it to the public with AB539884 vote".

2010/1/4	1	688	PLN	Juncus wallichianus	AB539884		Open	Sakura 2010/1/4	9	12244	BCT	Clostridium sp. C5S3,Clostridium sp. C5S7,Clostridium sp. C5S18,Clostridium sp. C5S4,Clostridium sp. C5S8,Clostridium sp. C5S10,Clostridium sp. C5S11,Clostridium sp. C5S17,Serratia sp. C5S9	AB539899		Open	Sakura 2010/1/4	1	744	PLN	Rhus chinensis var. roxburghii	AB539919	@@[organism]@@ genes for 18S rRNA, ITS1, 5.8S rRNA, ITS2, 28S rRNA, partial and complete sequence	Open	Sakura 2010/1/5	454	208648	EST	Seriola quinqueradiata	FS639517	Seriola quinqueradiata mRNA, clone: YTL6_H11, 3'-end EST, expressed in yellowtail liver	Open	MSS(gdb,adb) 2010/1/5	40	55561	ENV	uncultured archaeon,uncultured bacterium	AB539920	@@[organism]@@ gene for 16S rRNA, partial sequence, clone: AR80A22	Open	MSS(gdb,adb)

5. Who's submitting to Which Bank?


<DDBJstat> Patterned Submission <Pattern> To DDBJ From China<Period>2009-01-01/2009-12-31 <Occurence>42 <DDBJstat> Patterned Submission <Pattern> To GenBank From China<Period>2010-01-01/2010-12-31 <Occurence>6293 <Note>EST,GWS not counted <DDBJstat> Patterned Submission <Pattern> To EMBL From China<Period>2010-01-01/2010-12-31 <Occurence>97 <Note>EST,GWS not counted <DDBJstat> Patterned Submission <Pattern> To DDBJ From China<Period>2010-01-01/2010-12-31 <Occurence>36 <Note>EST,GWS not counted
 * It was not a number of array votes but each project (thesis) as for the data contribution to INSDC and it totaled, and the ratio in which DDBJ was used was measured from each country of the Asian Pacific Ocean.
 * In after parentheses of the name of a country, it is a number of ten years of total contribution projects.
 * Because it is 100% both, the registration of Japan and South Korea Patent Office has been excluded. **Moreover, a large amount of registration such as EST and WGS is not included in the convenience of the total.
 * (Takagi task ..order.. force TTF of Yasushi contents integration data base center re-analysis Watanabe in which data made INSDC contents (the 2nd) is analyzed again in the place where integrated data base center of DDBJ release (the 1st) data) Tamotsu Ohisa
 * Data File:DDBJstat_submission.doc all patterns in submissions every year summary. shown below is a part of it.   <DDBJstat> Patterned Submission <Pattern> To EMBL From China<Period>2007-01-01/2007-12-31 <Occurence>95<Note>EST,GWS not counted <DDBJstat> Patterned Submission <Pattern> To DDBJ From China<Period>2007-01-01/2007-12-31 <Occurence>20 <Note>EST,, GWS not counted <DDBJstat> Patterned Submission <Pattern> To GenBank From China<Period>2008-01-01/2008-12-31 <Occurence>8243 <Note>EST,GWS not counted <DDBJstat> Patterned Submission <Pattern> To EMBL From China<Period>2008-01-01/2008-12-31 <Occurence>78 <Note>EST,, GWS not counted <DDBJstat> Patterned Submission <Pattern> To DDBJ From China<Period>2008-01-01/2008-12-31 <Occurence>31 <Note>EST,GWS not counted <DDBJstat> Patterned Submission <Pattern> To GenBank From China<Period>2009-01-01/2009-12-31 <Occurence>8464 <Note>EST,GWS not counted <DDBJstat> Patterned Submission <Pattern> To EMBL From China<Period>2009-01-01/2009-12-31 <Occurence>92 <Note>EST,GWS not counted

Acceptance and pressing of opening to the public of demand of array registration vote opening to the public
charge [anote-tarisuto] Sakai [ka**] doctor (medicine) etiology and [rieeshima] Kimiko pathology major Mimura Sugita Mayumi
 * The array registration vote that accepts registration is hided secretly in DDBJ until the release date that the enrollee specifies.
 * The receipt number ([akusesshon] number) issued with DDBJ when registration is received is demanded from the examination of the cooked treatise. *The enrollee mostly makes a specified day slow and after confirming the thesis publication, directs DDBJ the array opening to the public by mail. *[Anote-ta-] directed opening to the public makes a specified day proceed to the system of opening to the public by using internal DB system TSUNAMI modification.
 * The thesis is published, and the array vote of the [akusesshon] number in the thesis is acquired when the author forgets reporting and the reader cannot acquire inspection.
 * The [akusesshon] number in the thesis is always observed by the method of the uncertainty in NCBI.
 * When a new [akusesshon] number for the DDBJ opening to the public is found, it contacts the charge of DDBJ.
 * When the array vote is a unopening to the public, the (Release request) opening to the public is advanced.
 * Charge [anote-ta-] confirms the thesis that exists in the report and being seen is confirmed.
 * It looks for whether the [akusesshon] of unopening to the public number is more in the same thesis. And,
 * 1) A thesis concerned is written and held in bibliography information on the array vote. (renewal of array vote)
 * 2) Opening to the public is reported to the author. Acknowledgment is not indispensable.
 * 3) TSUNAMI is advanced and the array of using concerned vote is advanced to the system of opening to the public.
 * This is changed to a thesis concerned when the array vote has opened to the public and it is written Unpublished in the field of the document (Update request).
 * When a specified release date is received before the thesis is published, opening to the public is advanced with DDBJ.
 * HiRDDBJ displays the list of the array vote that receives before ten days of a specified release date.
 * HiRDDBJ automatically puts out alert mail to the enrollee.
 * [Anote-ta] that receives answer (ML) changes a specified day according to the demand.
 * It advances to opening to the public when there is no change request and when there is no answer.
 * HiRDDBJ sweeps the [akusesshon] number list that receives a specified release date.
 * [Anote-ta] confirms the one that the assessment ended or the flag and confirms the presence of a special instruction concerning opening to the public.
 * The instruction of opening to the public is issued to HiRDDBJ if it follows, and there is no instruction if there is an instruction.

<EventStat> Release Request from NCBI <Period> 2010-01-01/2010-12-31 <Total events> 228 <Affected records> 28002 <EventStat> Update Request from NCBI <Period> 2010-01-01/2010-12-31 <Total events> 843 <Affected records> 794827 <EventStat> Release Request from Submitter <Period> 2010-01-01/2010-12-31 <Total events> ? <Affected records> ? <EventStat> Update Request from Submitter <Period> 2010-01-01/2010-12-31 <Total events> ? <Affected records> ?

UpdateLog

Change in content of array vote and style
Each pole always makes a change to the registration vote (DDBJ : to J-DDBJ) accepted by oneself. There are three kinds of changes about the following. (note)All the array votes have the unique identification number ([akusesshon] number) issued when registering. A mistake and an imperfect part might be corrected to the array of the array vote at the request of the enrollee, and to manage this, the principle adds the version number to this though it is invariable. The version number given when registration is accepted first is one. ex)AB123456.1
 * 1) the retrofit: The [akusesshon] number in which the change in the format that passes the discussion by three ultra practitioner conference is reflected even in the past is the state as it is.
 * 2) Upgrade: Correction and supplementation with base sequence done by request of enrollee. The version of the [akusesshon] number goes up and one goes up.
 * 3) the update: The [akusesshon] ..the addition and the change in the description (document etc.) in the array vote that does by the request of the enrollee.. number is the state as it is.

Retrofit

 * After it confers on the practitioner, Feature Table Definition (FTdoc) http://www.ddbj.nig.ac.jp/FT/full_index.html according to minutes that the fix is done receives the change.
 * First of all, the construction engineer modifies TSUNAMI according to FTdoc.
 * The item of the pull-down menu is added and corrected.
 * [Anote-ta] retrieves the array vote with the pattern that corresponds to the change object by using TSUNAMI.
 * The change is put directly with TSUNAMI when not is becoming empty of the number of array votes that become objects.
 * HiRDDBJ is replaced patterning use when there are a lot of numbers of array votes that become objects. YamatoSQL is used for this.
 * YamatoSQL assumes the [akusesshon] number list to be an eating verb as an object and eats [ta-geppatan] and the replacement pattern.
 * The changed array vote proceeds to the system of opening to the public again if it has opened it to the public.
 * Because this change is not reflected in the version number, the one with a different content will be included in the accumulation thing of a daily file on the record of same ID.
 * Because this change is not reflected in the version number, the one with a different content will be included in the accumulation thing of a daily file on the record of same ID.

<EventStat> Retro Fitting <Period> 2010-01-01/2010-12-31 <Total event> ? <Affected records> ?

Upgrade

 * The enrollee can already freely correct the DNA sequence described in the registered array vote.
 * The example) 1kb decided longer than it registered became 2kb.
 * The example) The uncertain base written by N turned out.
 * Request mail (ddbjupdt@) from the enrollee is received and charge [anote-ta] corrects it.
 * It is confirmed whether it is an original registrant in the mail address etc.
 * TSUNAMI is used for the correction.
 * After it corrects it, an advanced instruction to the system of opening to the public is put out to TSUNAMI for the array vote opened to the public.
 * The version of the [akusesshon] number of the array vote goes up when opening it to the public again and one goes up.
 * It hides it secretly until the release date as usual for the array vote before it opens it to the public. *The work completion mail is sent to the client.

<EventStat> Version up request <Period> 2010-01-01/2010-12-31 <Total event> 377 <Affected records> 377

Https://spreadsheets.google.com/a/g.nig.ac.jp/ccc?key=0AkgA4y3ofoc8dE1fZV9yNmRiQWlHLVpMR0cwTWk2d3c&hl=ja array update (2010/1/1?2010/12/31)

Update

 * The enrollee can already freely correct content other than the DNA sequence described in the registered array vote.
 * The example) The document is newly added.
 * The example) Because the gene name changed, it updates it.
 * The example) Because the scientific name of the living thing that was the new kind was decided, it describes.
 * Request mail (ddbjupdt@) from the enrollee is received and charge [anote-ta] corrects it.
 * It is confirmed whether it is an original registrant in the mail address etc.
 * TSUNAMI is used for the correction.
 * After it corrects it, an advanced instruction to the system of opening to the public is put out to TSUNAMI for the array vote opened to the public. *It hides it secretly until the release date as usual for the array vote before it opens it to the public. *The work completion mail is sent to the client.

Charge [anote-tarisuto] Sakai [ka**] doctor (medicine) etiology and [rieeshima] Kimiko pathology major Mimura Sugita Mayumi </ pre >

<EventStat> Update request from User <Period> 2010-01-01/2010-12-31 <Total event> ? <Affected records> ?

Coordinated business with Japan-South Korea Patent Office

 * It asks for a patent in treatment and the diagnosis and the inventor of the usage can ask for a patent a useful protein and the gene (..drinking.. array), etc.*The applied array and the usage are important and it is really new is important in the examination. *An indispensable "Sets of already-known arrays all over the world" for this examination is made by cooperating with the science organization in the United States, Europe, and South Korea and Patent Office every day and DDBJ is being offered to the world. *As a result, the array of the patent official report origin can also do the retrieval use for the thesis origin to the researcher without the array and the distinction. *In addition, the lease line is constructed between Japanese Patent Office and National Institute for Genetics, and the system safely comparable is operating data that Patent Office are in the application array and DDBJ of the unopening to the public.

Acceptance of array vote

 * 1) Sending from Patent Office (JPO)
 * 2) * 3or4 time data is sent from JPO to DDBJ every month by an irregular additional mail in addition to a regular flight of one time and 12 irregular flights.
 * 3) * It appends in the complaint among applications made when applying for the patent and array vote ST25 of the format that Patent Office provides is appended to the one including the array.
 * 4) * The array vote of announcing to public that passed three months after disclosing the patent official report applied for to Patent Office in Japan of a domestic announcing to public is sent collectively in the regular flight once a month.
 * 5) * The array vote of announcing to public that passed three months after opening announcing to public that is applied for the international announcing to public international and is sent to Patent Office in Japan to the public is sent collectively in the regular flight once a month.
 * 6) * When four months have passed since announcing to public that had been translated into Japanese of announcing to public whose it is a patent applied for in foreign countries of announcing to public of making public and Japan is a designated state opened it to the public, it is sent collectively by the regular flight.
 * 7) Sending from South Korea Patent Office KPO
 * 8) * The array vote of the South Korea Patent Office announcing to public is sent to KOBIC(Korean Bioinformatics Center) http://www.kobic.re.kr/(Director Dr.Sanghyuk Lee) every month.
 * 9) * The noise of filling in when applying being included in the array vote is removed with KOBIC. (Dr. Lee Byung Wook)
 * 10) It works later ..sending.. as well as this Patent Office * DDBJ.
 * 11) ** The mark of the irregularity type of the detection leakage of another type is repeatedly having a rough going to the first time registration opening two years ago to the public a little by repeating the re-being found re-[totono] type opening to the public now.

Acceptance and processing opening to the public

 * The array vote of the DDBJ type is made from 特許庁配列票 of DDBJ [dehako].
 * Patent Office mends the living thing name etc. not controlled as much as possible ..standard scientific name (NCBI-TAxonomy)...
 * The array of N alone that doesn't fill the standard of INSDC and the array of several characters are excluded, and duplicate registration is investigated.
 * The [akusesshon] number (INSDC array vote ID) is issued to the one to fill the standard and it sends it to Patent Office.
 * It throws to the system of opening to the public at once. The above-mentioned process is done within three days usually.
 * The exchange opening to the public is done by three poles as a daily file and it is included in the next release. It is made to the object of the word search and BLAST without the distinction.

History <Event>Patent <Date>1993-04-xx <Note> EPO､USPTO sequence data released in DDBJ Release 13 <Event>Patent <Date>1993-07-xx <Note> JPO sequence data included in DDBJ Release 14 <Event>Patent<Date> 1997-05-xx <Note> at ICM10th, representatives from JPO/EPO/USPTO attend and agreed in using(DDBJ/EMBL/GenBank)as framework of exchanging and sharing USTPO,EPO,JPO data. <Event>Patent <Date> 2006-07-xx <Note>JPO contacted DDBJ on KIPO data sharing via DDBJ <Event>Patent <Date> 2007-xx-xx <Note> Prof. H.Sugawara visited KOBIC on data transfer. <Event> Patent <Date> 2008-03-xx <Note> Sequence data from KIPO released from KOBIC->DDBJ. <Event> Patent <Date> 2009-07-xx <Note> Mr.Aono assigned as DDBJ Patent leader/Hub <Event> Patent <Date> 2009-07-xx <Note> web site for patent business started by editor Mr. Aono <Event> Patent <Date> 2010-05-xx <Note> DDBJ started to put taxonomyID to patent derived records. <Event> Patent <Date> 2010-05-xx <Note> amino acids in patent file put on anonymous ftp. <Event> Patent <Date> 2010-07-xx <Note> K.Okubo visited KOBIC on data transfer <Event> Patent <Date> 2010-08-xx <Note> patent amino acids subjected to DDBJ-Blast

=Life sequence data archive business (note) started up in consignments other than project expense=
 * pages in English:DDBJ Raw sequence data Archive
 * The raw data archive of machine enrollee's information "* DDBJ is an archive in life sciences for a long time for preservation and sharing the raw data that an automatic sequencer makes. * International Sequence Database Collaboration (INSDC) It is a part of the business.

Procedure of registration

 * The account application is gotten from DDBJ and a peculiar account to the registration sequence center is made.
 * Please make the meta data on Web.
 * Shape tells incompleteness by mail in a mechanical check.
 * Mr. Saruhashi is checking the correspondence of the support of registration and the field and the value.


 * The ACC number is issued.
 * As for the orchis data, please do scp from the made account to the DDBJ server.
 * It converts it into SRA-full with DDBJ. If the error happens, it reports.
 * If the release date comes, it opens to the public from DDBJ, and SRA-full and the meta data are sent to NCBI.

Trace Archive at DDBJ (DTA)JST BIRD project

 * It is an archive business intended for the lead file of the sequencer (next generation former) that separates a reactive thing to use the Sanger method by electrophoretic.
 * The lead file is one analytical result file generated when one http://trace.ddbj.nig.ac.jp/DTASearch/trace?ti=2282248605 [konoyouna] [tan] reaction is analyzed. An automatic sequencer generates hundreds of lead files from tens of with driving once.
 * From tens of in the length of the base to about ..size of hundreds of base file.. 200 the KB. the data size of the lead file

operation charge [anote-ta] Kodama [**] [kazuhiroshi] (bioscience) bioscientific subject 2007 moat Takashi of five representative [**] that entrusted development from MEXT integration data base project

When registering in DDBJ

 * Table information and data are kept in DDBJ and NCBI, EBI, and DDBJ become possible to offer the retrieval anywhere it.
 * DDBJ sends NCBI the table and the lead file first accepted.
 * ID is issued to each lead file in NCBI that issues ID to the return and it is sent back to DDBJ.
 * DDBJ manages data though this ID is used and it is local.
 * EBI also sends the registration of the trace to acceptance NCBI as well as DDBJ.
 * It doesn't go in DDBJ though EBI mirrors the data registered in NCBI at the same time.
 * Please retrieve it with NCBI or EBI when you want to retrieve a trace all over the world.
 * Retrieval DL is similarly possible from anywhere to want to see the trace registered in DDBJ and to acquire it of three people.

Size of DTA

 * The trace file is 2.1 billion lead http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=graph_query&m=stat&s=graph files and in NCBI as of January, 2011 with.
 * The data sizes are 200 terabites in the compressed ftp site.
 * The number of traces registered by way of DDBJ is about five million lead files.
 * It is total 500Giga byte and 1/400 of NCBI by four kinds of fasta metadata scf quality data of the compressed format.
 * The retrieval operating with DDBJ and the compression acquisition system of a lot of files are making by oneself. It made it from MySQL (Small [takun] Mr. Fukuda :). **Because the enterprise cannot use MySQL by free, it is operated with HiRDB (Specifications when developing are in clerical work).
 * It is possible to use it up to 100 million usually when assuming that the acceptance is the time none even if nothing is done. (Fukuda)**It is possible to move to the machine of high specs without fiddling with anything. However, it is proportionally late at that time. **It makes to the parallel to reduce this inclination and there is a doing way. put the index data on the memoryThe work generation of new is done. It seems that it is 5?6 man.month. (Ogasawara Fukuda)
 * When registration is received, correspondence to a domestic sprinkling should be able to be made with enrollee [gawa] in case of the acceptance of an organization ..holding very much.. big when increasing because one Mr. Kodama is correspondence ..that.. ..the nun...
 * If apache Thora (ARSA substitution) is handled, it is sure to be able to do by even two billion(Ogasawara).

Procedure of DTA registration

 * Items that should be described are about ten items though the meta data has the type division and 89 item kind etc. of the living thing of the research. The description of the enrollee and the contact of the feature is unnecessary, and the field written in the free style type for the name of the sequence center to take the place of it is roughly blanks.
 * The enrollee makes the meta data based on the template.
 * The account application is gotten from DDBJ and a peculiar account to the registration sequence center is made.
 * The lead file and the meta data are collected to the account on putting DDBJ side and it checks it.


 * This archive business is a part of the life science integration data base project, it is supported to center (BIRD) of promotion of the bioinformatics of the science and technology promotion mechanism, and it executes it.

=Registration, analytical support system pipeline development, and operation (http://p.ddbj.nig.ac.jp DDBJ Read Annotation Pipeline)=
 * The fixed form analysis pipeline is constructed in the computer system of DDBJ to support the sequencing analysis of a new sequencer and it is offering it.
 * The basic processing part function: The mapping on the de novo assembly and the reference is being offered. (De facto standard program is prepared. )
 * The higher-order processing part function: Workflow of the SNP detection using galaxy, the RNA-seq analysis, and the ChIP-seq analysis is supported.
 * The Cloud function: As for the user, a large-scale analysis for which the inheritance laboratory super computer is used by accessing by way of a WWW browser is possible.
 * 2010年開発分の報告

=Business system and new development =
 * It develops in DDBJ according to the change in not only the operation of the business but also the demand.

INSD accompanying new data base BioProject

 * It is desirable to undertake the diversification of registration with the frame of INSD and to manage some fields of the DDBJ record by an outside data base.
 * It is NCBI-Taxonomy in an old example. To write the taxonomical tree and the new kind frequently rewritten in the SOURCE line, this is made from another NCBI data base.
 * In ICM 20th(2007), NCBI Genome Project data base now at the time of targeted genome project was greatly enhanced, and it ..' BioProject '.. agreed to construct the data base with three ultra cooperation intended for the project whole.
 * The XML schema that used this for the description method of BioProject by three ultra receiving cooperation was settled on at current year.
 * The acceptance of the big project in Japan was made in DDBJ and to do the management description by the world standard, the website of  DDBJ-BioProjectwas made.
 * Moreover, the conversion program from the Excel file and the Excel file to the XML file that accepted new BioProject registration was made.
 * The beginning of mission is a schedule in the coming year.

開発仕様決定　李慶範、児玉悠一、真島淳 構築システムエンジニア　DBT

New sequencer fixed quantity data base DOR(DDBJ Omics ARchive)

 * CIBEX (Center for Information Biology gene EXpression database) is operated the microarray data registration in DDBJ.
 * Tag count data by the next generation sequencer that archive is done by raw data?Archive [subeku] and DDBJ Omics Archive (DOR) is newly planned.
 * DOR adopts MAGE-TAB that FGED (Functional Genomics Data) Society settled on as well as ArrayExpress of EBI as a meta data form, and has exchanged data for DOR between ArrayExpress.
 * The data stored in CIBEX exports to ArrayExpress one by one, too.
 * The data management screen of DOR and the data sending system to ArrayExpress were constructed within 2010, and the CBX69 data of CIBEX was exported to ArrayExpress as E-DORD-69. []
 * Progress in 2010
 * The inner system that manages an export of the DOR data and a new receipt of data is constructed.
 * The export system for the data exchange with ArrayExpress is constructed.
 * Preparation for new receipt system to issue DOR original accession.

企画　中村保一　神沼英理　児玉友一 開発

Construction of single sign-on environment
Single sign-on is a function to finish the user attestation of two or more tools only once as for the input of the password and ID. To finish the user attestation in the tool of registration, the retrieval, and the analysis of DDBJ once, the single sign-on environment by OpenSSO was developed. Development begins in March, 2010, and it has mounted on the basic processing part of DDBJ Pipeline and the connection of the accompanying program now. It is scheduled to apply it to new getentry and new SAKURA under development in the future.

企画　　神沼英里　中村保一 開発　　DBTエンジニア 山本圭介、新山雪絵

= DDBJスーパーコン入れ替えと業務移行に向けた業務ソフトウェアの見直し 「高木タスクフォース」=
 * DDBJ構築系 and DDBJ公開系 have been served by the business request to the enterprise in the past 20 years in DDBJ (It is).
 * Existing DDBJ business software depends on specific contractor's middleware and hardware.
 * When the researcher of the biotechnology system does a large-scale information processing business for the short term, it is an effective selection.
 * However, it is assumed that this state is generally called "Vendor lock-in", and it deprives of degree of freedom and flexibility in long-term operation, and it causes total cost. (reference)
 * Original development of the system of opening to the public began in "Takagi task force" organized to get rid of this Vendor lock-in with open source software.
 * Software that played a center role of "Opened to the public" business was originally developed in the flow of receipt (2) of the (1) data of the DDBJ business assessment (3) opening to the public at current year.
 * タスクフォース: 山田弘明  宗像善久　白石直樹　渡邊康司　小笠原理 高木利久

Task 1: Redevelopment of retrieval of the W-DDBJ latest release (present ARSA)

 * Present search engine (ARSA) (introduction in 2007) uses Interstage Shunsaku Engine of Fujitsu Ltd. (hardware only for the retrieval).
 * It was a point that a lot of data base votes were able to be integrated into a no structure and a system attractive scalable etc. unnecessary the index and easily to operate.
 * It becomes impossible to deal with the increase and the diversification of the number of INSDC(W-DDBJ) records however by the scalability for which the budget that which is unexpectedly explosive and proportional to volume of data is necessary.
 * The feature of Shunaku now though the retrieval of making the best use of many kinds of data bases high-speed and simultaneously is being offered
 * "Data of the half one's life" of huge numbers such as EST, GSS, and WGS has come off from the retrieval object on the other hand in essential INSDC(W-DDBJ).

Improvement of expansion retrieval speed of data size in which system of open source can be retrieved It is a function that it operates on a general Linux server and the adjustment of the detail like the offer of WebAPI of the search engine that enables two expression operation simultaneously (When the DDBJ data release is opened to the public, the search engine is not stopped for the data replacement) besides, the addition of the Fassett retrieval function, and the function of the ranking of the retrieval result, etc. etc. expand.
 * The development specification point across current year and the coming year is that becomes it as follows

開発仕様作成　小笠原理、高木利久 開発受託　(株）プリファードインフラストラクチャー

Task 2: Redevelopment of data base (present getentry) with history management function of W-DDBJ

 * The service of the exit to which the user takes out the array registration vote by the accession number (inspection download) : now.
 * Redevelopment requirement


 * It shifts to the system of not specific contractor's Relational Database Management System but open source.
 * The recording function and the display function of update history information on the data that DDBJ disclosed (revision number) are added.
 * Function corresponding to sequence revision history of GenBank.
 * Stipulation and mounting of method of operating management opened to the public.

開発仕様作成　小笠原理、高木利久 開発受託　(株）プリファードインフラストラクチャー

Task 3: Redevelopment of DDBJ daily update program
開発仕様作成 小笠原理、宗像善久、白石直樹、高木利久 開発受託 (株）情報数理研究所
 * The conversion program and the check program are mounted again in shape to lose the specific contractor's dependence on Relational Database Management System.
 * The source code etc. of the business program of the format definition document and DDBJ are reexamined, and work to make the specification of conversion and the check an express statement is done.

About one year in the coming year after the test operation and it adds it the function and it is scheduled to operate it these.
 * ARSA redevelopment version (Be adjusting it) http://pfi1.genes.nig.ac.jp/html/QuickSearch

Task 4: Investigation and experiment for DDBJ new super computer system design
山田弘明 宗像善久　白石直樹　渡邊康司　小笠原理　高木利久　(以上高木タスクフォースTTF)
 * The present business process was analyzed for the design of the new super computer system scheduled in 2013 and the relation and the technology investigations and the experiment use for a new technology were done.


 * The document and the source code are collected.
 * When the review was advanced, the operation document of a present system and the source code were collected in one place. (Part is unincluded in the library etc.)


 * Collection of data that becomes IN/OUT for DDBJ
 * To do handiness when, data shifted and worker's trials handily, INSD and the exchange data such as Patent Office were collected in one place turning ..seeing to the person related to DDBJ... (The release data of DDBJ, EMBL-Bank, and GenBank is omitted as big as the size. )


 * Confirmation of periodic release business details flow
 * Collected manuals and source codes of the use program were one by one confirmed, and the periodic release business investigation and the documentation work were done. The flow of processing was put into writing while considering what to be consisting meaning it of processing concerned in the shape that did not depend on a current mounting as much as possible based on information within the ranges that were able to be collected because details why it is such mounting were lost about the program, and there was a part where a clear meaning of the program became uncertain, too ( the making one appendix 定期ﾘﾘｰｽ procedure Naoki by Shiraishi Munakata good Hisashi). The verification work will be done based on the made document in the future.


 * Operation of system of present periodic release business situation analysis
 * Various load situations of the business concerned server at the periodic release business of present were confirmed, and the bottleneck of processing was analyzed. (付録１定期リリース作成手順 by 白石直樹　宗像善久)


 * Feasibility investigation of new, decentralized software technology
 * To high-speed process it with a cost performance high, small-scale server, the propriety of the application of the new, decentralized software technology such as Hadoop was investigated for mass release data. （付録2現行システム調査　by 白石直樹　宗像善久）


 * Analysis of DDBJ assessment business TSUNAMI Dataflow log mailing list log
 * An analytical investigation of the log was done for the DDBJ assessment business analysis.


 * Investigation of IT infrastructure situation of foreign countries and others site
 * The IT infrastructure situation of the site related to overseas NGS such as Sanger and BGI was investigated. (付録3海外サイト状況　by 宗像善久)

=Open use for computer system=

Open system project

 * It lends it by receiving the increase of the data processing demand to like big parallel processing of the scale in the life field, and dividing the PC cluster with most demands that DDBJ has in 2009 flexibly.
 * Up to now..go..memory..big..computer..environment..division..long term..loan..discontinue..manage..pipeline..assign..god.

企画　高木利久 運用　システム管理チーム　竹井和也、奈倉雅彦


 * It is possible to use it for large scale length time analytical processing and the software development of making to the parallel.
 * Topics of research are regularly recruited, hoped content of the research theme and computer resource and use hope time, etc. are examined overall, and right or wrong of the adoption is decided.
 * The offering circular is posted in the http://www.ddbj.nig.ac.jp/index-j.html DDBJ homepage at the time of beginning of fiscal year. Moreover, we will tell it by the Maling list.
 * The use results of the researcher who belongs besides the inheritance laboratory are as follows. (Belonging and the official position are the one at the time of the application. )


 * 1) The announcement was requested from the following organizations so that place inside and outside user might learn the open system project.
 * JBIC ..[rumaga] (.. [rumaga] [**] [noirai])
 * DDBJ e-mail magazine (e-mail magazine publishing request)
 * JSBi (member individual announcement request)
 * Bioinformatics-jp (member individual announcement request)#The system management team will individually catch will do contact and the needed environment, and we help construction in the researcher of the problem that was going to be adopted as follows.
 * User account making
 * NQS cue making (The cue making of Oracle Grid Engine is included). #:* Disk area making
 * Firewall setting
 * OpenMPI environmental setting/confirmation

=External announcement human resources development announcing to public = 企画　神沼英里　中村保一

External announcement

 * The DDBJ business and development were announced as follows.

<Event> Academic presentation <Date> 2010-12-07 <Place> meeting= 第33回日本分子生物学会年会 ランチョンセミナー, Place= 神戸国際展示場 <Note> Title= 「DDBJ / INSDC の新型シーケンサデータへのとりくみ "DDBJ Sequence Read Archive (DRA) と解析支援系 DRA pipeline"」 <Note> Author= 中村　保一

<Event> Academic presentation <Date> 2010-12-07 <Place> meeting= 第33回日本分子生物学会年会 ワークショップ 1W20-p, Place= 神戸国際展示場 <Note> Title= 「新型シーケンサーから得られるデータをどう解釈し活用するか：統合データベースプロジェクトからの提案」 <Note> Author= 中村　保一・坊農　秀雅

<Event> Academic presentation <Date> 2010-12-07 <Place> meeting= 第33回日本分子生物学会年会 ワークショップ 1W20-p-1, Place= 神戸国際展示場 <Note> Title= 「DDBJ Sequence Read Archive (DRA) と DRA Annotation Pipeline: 新型シーケンサへの DDBJ の対応」 <Note> Author= 神沼 英里，望月 孝子，児玉 悠一，猿橋 智，菅原 秀明，大久保 公策，高木 利久，中村 保一

<Event> Academic presentation <Data> 2010-12-08 <Place> meeting= 第33回日本分子生物学会年会 ポスター発表 2P-1203, Place= 神戸国際展示場 <Note> Title= 「DDBJ Sequence Read Archive / DDBJ Omics Archive」 <Note> Author= 児玉　悠一，猿橋　智，坂井　勝呂，神沼　英里，菅原　秀明，高木　利久，大久保　公策，中村　保一

<Event> Academic presentation <Data> 2010-12-07 <Place> meeting= 第33回日本分子生物学会年会 ポスター発表 1P-0713, Place= 神戸国際展示場 <Note> Title= 「DDBJ Read Annotation Pipeline: 新型シーケンサ由来配列データ解析パイプライン」 <Note> Author= 望月 孝子，児玉 悠一，猿橋 智，神沼 英里，菅原 秀明，大久保 公策1，高木 利久，中村 保一

<Event> Academic presentation <Date> 2010-11-29 <Place> meeting= Workshop title: Toward next generation studies of biodiversity and bioresources. As 2010 Collaborative Research and Research Meeting, National Institute of Genetics, Research Organization of Information and Systems Place= Mishima, Shizuoka <Note> Title= "DDBJ Sequence Read Archive and a cloud-computing based analytical pipeline" <Note> Author= Kaminuma,E.

<Event> Academic presentation <Date> 2010-11-10 <Attendant> <Place> meeting= 生命情報若手の会第2回研究会, Place= 静岡県三島市 <Note> Title= DDBJ Read Annotation Pipeline　次世代シーケンサ由来配列データ解析パイプライン　解析目的別ワークフローの構築 <Note> Author= 望月　孝子, 児玉　悠一, 猿橋　智, 長崎　英樹, 神沼　英里, 菅原　秀明, 大久保　公策, 高木　利久, 中村　保一

<Event> Academic presentation <Date> 2010-10-12/2010-10-13 <Place> meeting= Fourth Biocuration Conference, Place= Odaiba, Tokyo, Japan <Note> Title= Gene Trek in Prokaryote Space (GTPS) reduces GIGO in the annotation of microbial genome sequences <Note> Author= Kosuge,T., Shigemoto,Y., Kuwana,Y., Sugawara,H.

<Event> Academic presentation <Date> 2010-10-12/2010-10-13 <Place> meeting= Fourth Biocuration Conference, Place= Odaiba, Tokyo, Japan <Note> Title= DDBJ Sequence Read Archive / DDBJ Omics Archive <Note> Author= Kodama,Y., Saruhashi,S., Kaminuma,E., Sugawara,H., Takagi,T., Okubo,K., Nakamura,Y.

<Event> Academic presentation <Date> 2010-10-05 <Place> meeting= 統合データベースプロジェクトシンポジウム「ライフサイエンスの未来へ～10年先のデータベースを考える～」, Place= 東京大学本郷キャンパス浅野地区　武田先端知ビル５Ｆ　武田ホール　（東京都） <Note> Title= 「DDBJ Sequence Read Archive / DDBJ Omics Archive」 <Note> Author= 児玉　悠一、猿橋　智、神沼　英里、菅原　秀明、高木　利久、大久保　公策、中村　保一

<Event> Academic presentation <Date> 2010-10-14 <Place> meeting= NIAS Symposium RAP7 meeting, Place= Tokyo International Exchange Center, Tokyo, Japan <Note> Title= DDBJ Read Annotaion Pipeline: A cloud computing based analytical tool for next-generation sequencing data <Note> Author= Nakamura,Y., Kaminuma,E., Mochizuki,T., Kodama,Y., Saruhashi,S., Nagasaki,H., Sugawara,H., Takagi,T., Okubo,K.

<Event> Academic presentation <Date> 2010-09-15/2010-09-19 <Place> meeting= The tenth Cold Spring Harbor Laboratory/Wellcome Trust conference on Genome Informatics, Place= Hinxton, UK; poster <Note> Title= DDBJ Sequence(発表時追加) Read Annotation Pipeline A cloud computing-based analytical tool for next-generation sequencing data <Note> Author= Kaminuma,E.1, Mochizuki,T.1, Kodama,Y.1 , Saruhashi,S.1 , Sugawara,H.1, ( Okubo,K.1,2 , Takagi,T.1,2 and Nakamura,Y. 1 Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Japan( 2  Database Center for Life Science, Tokyo, Japan

<Event> Academic presentation <Date> 2010-09-10 <Place> meeting= ゲノムテクノロジー第164委員会 第34回研究会「次世代シークエンサーの衝撃」　Place= 霞山会館　（東京都） <Note> Title= 「次世代シーケンサ由来データの公的アーカイブと利用・解析 - DDBJ Sequence Read Archive & DDBJ Pipeline - 」 <Note> Author=児玉　悠一

<Event> Academic presentation <Date> 2010-09-09/2010-09-10 <Place> meeting= 第148回農林交流センターワークショップ「次世代シーケンサーを利用したゲノム解析の実際」　Place= 農林水産省農林水産技術会議事務局筑波事務所　（つくば市） <Note> Title= 「次世代シーケンサーのアーカイブDBとクラウド型データ解析システムの紹介」 <Note> Author=神沼　英里, 児玉　悠一, 望月　孝子, 猿橋　智, 長崎　英樹, 菅原　秀明, 大久保　公策, 高木　利久, 中村　保一

<Event> Journal paper <Date> 2010-08 <Note> Title= Biological databases at DNA Data Bank of Japan in the era of next-generation sequencing technologies <Note> Author= Kodama Y, Kaminuma E, Saruhashi S, Ikeo K, Sugawara H, Tateno Y, Nakamura Y.  <Note> Citation= Advances in Experimental Medicine and Biology, 2010, Vol. 680, Part 1, 125-135

<Event> Academic presentation <Date> 2010-07-13/2010-07-15 <Place> meeting= 13th International MGED Meeting (MGED13), Place= Boston, MA, USA <Note> Title= DDBJ Omics Archive and DDBJ Read Annotation Pipeline: archive and analyze quantitative data from next generation platforms, <Note> Author= Kodama,Y., Kaminuma,E., Mochizuki,T., Bono,H., Sugawara,H., Takagi,T., Okubo,K., Nakamura,Y.,

<Event> Academic presentation <Date> 2010-07-09-- <Place> meeting= 18th Annual International Conference on Intelligent Systems for Molecular Biology(ISMB2010), Place= Boston, MA, USA <Note> Title= DDBJ Read Annotation Pipeline: A web-based analytical tool for next-generation sequencing data <Note> Author= Kaminuma,E., Mochizuki,T., Kodama,Y., Saruhashi,S., Sugawara,H., Okubo,K., Takagi,T., Nakamura,Y.

<Event> Academic presentation <Date> 2010-07-02 <Place> meeting= NIASシンポジウムイネ遺伝学・分子生物学ワークショップ2010プログラム, Place= つくば国際会議場 <Note> Title= 「次世代シーケンサのアーカイブDBとクラウド型解析パイプライン」 <Note> Author= 神沼　英里・望月　孝子・児玉　悠一・猿橋　智・菅原　秀明・大久保　公策・高木　利久・中村　保一

<Event> Journal paper <Date> 2010-01 <Note> Title= DDBJ launches a new archive database with analytical tools for next-generation sequence data <Note> Author= Kaminuma E, Mashima J, Kodama Y, Gojobori T, Ogasawara O, Okubo K, Takagi T and Nakamura Y. <Note> Citation= Nucleic Acids Research, 2010, Vol. 38, Database issue D33-D38

<Event> Journal paper <Date> 2010-01 <Note> Title= Archiving next generation sequencing data <Note> Author= Shumway M, Cochrane G and Sugawara H. <Note> Citation= Nucleic Acids Research, 2010, Vol. 38, Database issue D870-D871

Course
<Event> lecture <Date> 2011-01-17/2011-01-18 <Place> meeting= 23rd DDBJing, Place= 長浜バイオ大学 語学実習室　（滋賀県長浜市） <Attendant> ... <Note> Title= 「DDBJ の紹介と大量配列のためのクラウド型計算機資源利用法」　<Note> Autehor= 中村　保一 <Note> Title= 「次世代シークエンサ(NGS)概論とクラウド型解析ツール DDBJ Pipeline」　<Note> Author= 神沼　英里 <Note> Title= 「NGS 登録データベース DDBJ Sequence Read Archive」　<Note> Author= 猿橋　智 <Note> Title= 「NGS クラウド型解析ツール DDBJ Pipeline 実習」　<Note> Author= 望月　孝子 <Note> Title= 「SAKURA を用いた塩基配列登録の方法・実習」　<Note> Author= 真島　淳
 * DDBJ has held the course of the registration method and use of DNA data.
 * Current year..as follows

<Event> lecture <Date> 2010-08-09 <Place> meeting= ライフサイエンス・データベース講習会 －in 名古屋－, Place=名古屋大学 <Note> Memo= (2010年8月9日(月),10日(火)、名古屋大学・東山キャンパス・情報文化学部棟) <Note> Title= 「DDBJ past and future」 <Note> Autehor= 大久保　公策 <Note> Title= 「DDBJの新型シーケンサへの対応 ―データアーカイブ DDBJ Sequence Read Archive (DRA) と解析パイプライン」 <Note> Author= 中村　保一 <Note> Title= 「Parsing the Legacy DDBJ-- old but new」 <Note> Autehor= 小笠原　理 <Note> Author= 高木　利久, 川本　祥子, 畠中　秀樹, 山口　敦, 中尾　光輝, 大久保　公策,中村　保一, 小笠原　理, 中村　春木, 金城　玲, 鈴木　博文 加藤　和貴, 藤　博幸, 木下　賢吾, Daron M.Standley

<Event> lecture <Date> 2010-08-04/2010-08-15 <Place> meeting= DBCLS講習会 AJACS21 陸奥, Place= 東北大学 <Note> Title= 「次世代シークエンサの活用法/データの解析法」 <Note> Autehor= 中村　保一

<Event> lecture <Date> 2010-07-15 <Place> meeting= 第3回シーケンサー利用技術講習会, Place= 理化学研究所 横浜研究所 <Note> Title= 「次世代シーケンサーデータのDRA(DDBJ Read Archive)への登録」 <Note> Author= 児玉　悠一

<Event> lecture <Date> 2010-06-24 <Place> meeting= 22nd DDBJing, Place= ライフサイエンス統合データベースセンター <Attendant> ... <Note> Title= 「DDBJの紹介と配列データの検索」　<Note> Autehor= 中村　保一 <Note> Title= 「次世代シーケンサのクラウド型解析パイプライン」　<Note> Author= 神沼　英里 <Note> Title= 「次世代シーケンサアーカイブDB」　<Note> Author= 児玉　悠一 <Note> Title= 「クラウド型解析パイプライン・実習assembly/mapping」　<Note> Author= 望月　孝子 <Note> Title= 「SAKURAを用いた塩基配列登録の方法・実習」　<Note> Author= 小菅　武英 <Note> Title= 「相同性検索と系統解析：BLASTとClustalW」　<Note> Autehor= 中村　保一

<Event> lecture <Date> 2010-06-21 <Place> meeting= 第309回CBI学会研究講演会, Place= 東京工業大学　蔵前会館　ロイヤルブルーホール <Note> Title= 「DDBJ Read Archive (DRA) の紹介」 <Note> Autehor= 児玉　悠一

<Event> lecture <Date> 2010-06-07-2010-06-09 <Place> meeting= 2010 The 21th International Conference on Arabidopsis Research, Place= Yokohama, Japan <Note> Title= Plant SNP annotation using a web-based pipeline tool for next -generation sequencing data <Note> Author= Kaminuma,E.1; Mochizuki,T.1; Kodama,Y.1; Saruhashi,S.1; Sugawara,H.1; Okubo,K.1,2; Takagi,T.1,2; Nakamura,Y.1 (1.National Institute of Genetics, 2.Database Center for Life Science)

<Event> lecture <Date> 2010-06-04 <Place> meeting= DBCLS講習会 AJACS18, Place= 日本大学生物資源科学部 ２号館231教室　（湘南） <Note> Title= 「次世代シークエンサの活用法」 <Note> Author= 神沼　英里、望月　孝子、児玉　悠一、猿橋　智、菅原　秀明、高木　利久、大久保　公策、中村　保一

<Event> lecture <Date> 2010-05-26 <Place> meeting= 第5回 NIG内部交流会 DRAポスター発表, Place= 静岡県三島市 <Note> Title= 「DDBJ Read Archive ～次世代シークエンサからの出力データのためのアーカイブ～」 <Note> Author= 猿橋　智、児玉　悠一、神沼　英里、五條堀　孝、高木　利久、大久保　公策、菅原　秀明、中村　保一

<Event> lecture <Date> 2010-05-26 <Place> meeting= 第5回 NIG内部交流会 DRAポスター発表, Place= 静岡県三島市 <Note> Title= 「DDBJ Read Annotation Pipeline �0A Cloud computing based Analysis System for the Next Generation Sequencing Data�0」 <Note> Author= Mochizuki,T.; Kaminuma,E.; Kodama,Y.; Saruhashi,S.; Sugawara,H.; Okubo,K.; Takagi,T.; Nakamura,Y.

<Event> lecture <Date> 2010-05-26 <Place> meeting= 第5回 NIG内部交流会 DRAポスター発表, Place= 静岡県三島市 <Note> Title= 「協調作業・共同研究コラボレーション・ツールとしてGoogle AppsのDDBJにおける利用例�”DDBJからNIG全体への利用をめざして”」 <Note> Author= Kosuge,T.; Mochizuki,T.; Watanabe,S.; Mashima,J.; Kaminuma,E.; Okubo,K.; Takagi,T.; Nakamura,Y.

<Event> lecture <Date> 2010-03-19 <Place> meeting= 第51回日本植物生理学会年会　 データベース講習会, Place= 熊本大学 <Note> Title= 「次世代シークエンサデータのアーカイブ登録と解析パイプライン」 <Note> Author= 神沼　英里、望月　孝子、児玉　悠一、猿橋　智、菅原　秀明、高木　利久、大久保　公策、中村　保一

<Event> lecture <Date> 2010-02-18 <Place> meeting= 第2回シーケンサー利用技術講習会, Place= 理化学研究所 横浜研究所 <Note> Title= 「次世代シーケンサーデータのDRA(DDBJ Read Archive)への登録」 <Note> Author= 児玉　悠一

Visit guide

 * The visit request from the outside is always accepted in DDBJ.

DDBJ見学者リスト <Event> SiteVisit2010nn <Date> 2010-01-21 <Attendant> 李、村形、神沼 <Note> visitor=韓国・江原大学校 <Event> SiteVisit2010nn <Date> 2010-02-25 <Attendant> 神沼 <Note> visitor=淡島水族館 <Event> SiteVisit2010nn <Date> 2010-03-11 <Attendant> 中村 <Note> visitor=東京大学　植田教授 <Event> SiteVisit2010nn <Date> 2010-03-12 <Attendant> 舘野 <Note> visitor=医薬品産業情報研究会(PIフォーラム) <Event> SiteVisit2010nn <Date> 2010-03-25 <Attendant> 中村、神沼、望月、DDBJ構築チーム女性アノテータ <Note> visitor=お茶の水女子大学　瀬々研究室 <Event> SiteVisit2010nn <Date> 2010-03-30 <Attendant> 大城戸、柳楽 <Note> visitor=北海道札幌南高校 <Event> SiteVisit2010nn <Date> 2010-04-14 <Attendant> 五條堀、大久保、菅原 <Note> visitor=中国科学院 <Event> SiteVisit2010nn <Date> 2010-05-14 <Attendant> 舘野 <Note> visitor=三島市役所 民生委員 <Event> SiteVisit2010nn <Date> 2010-06-03 <Attendant> 中村 <Note> visitor=中央水産研究所 <Event> SiteVisit2010nn <Date> 2010-07-13 <Attendant> 中村 <Note> visitor=沖縄県産業振興公社 <Event> SiteVisit2010nn <Date> 2010-07-14 <Attendant> 中村 <Note> visitor=台湾NCKU <Event> SiteVisit2010nn <Date> 2010-07-26 <Attendant> 中村 <Note> visitor=JICA研修 <Event> SiteVisit2010nn <Date> 2010-08-24 <Attendant> 中村 <Note> visitor=榛原高校 <Event> SiteVisit2010nn <Date> 2010-08-27 <Attendant> 舘野 <Note> visitor=静岡県理科教員見学 <Event> SiteVisit2010nn <Date> 2010-09-30 <Attendant> 中村 <Note> visitor=三島市北上中学生徒見学 <Event> SiteVisit2010nn <Date> 2010-10-22 <Attendant> 大久保 <Note> visitor=文科省研究振興局学術機関課長による遺伝研の訪問（ＤＤＢＪ説明：大久保対応） <Event> SiteVisit2011nn <Date> 2010-12-27 <Attendant> 神沼 <Note> visitor=Han Bin（髣斌）先生 <Event> SiteVisit2011nn <Date> 2011-01-21 <Attendant> 小笠原、真島、児玉、他（アノテータ取材対応） <Note> visitor=理系漫画家はやのん　（DDBJの紹介漫画が日刊工業新聞に掲載: 2011/2/21: 添付参照） <Event> SiteVisit2010nn <Date> 2011-03-07 <Attendant> 大久保 <Note> visitor=愛媛大学・学部生(数名)による遺伝研の訪問（ＤＤＢＪ説明：大久保対応）

Data release news flash mail magazine newsletter
To pass on bank information to the user, information by three kinds of is distributed in DDBJ.

Data release news flash
We will inform you by the news flash when the large-scale registration that [anote-ta-] Mashima selected of should the attention is opened to the public. Address: DDBJ　Top　page； Hot Topics　と　Twitter（2010.04以降配信）（現在：約１００名，リスト：１１） <Event> DDBJ Hot Topics <Date> 2010-12-25 <Note>　未培養好熱 性アーキアゲノム配列の公開 <Event> DDBJ Hot Topics <Date> 2010-10-13 <Note>　ハボタン (Brassica oleracea var. acephala) EST 119,204 エントリの新規公開 <Event> DDBJ Hot Topics <Date> 2010-07-28 <Note>　分裂酵母 (Schizosaccharomyces pombe) GSS 113,551 エ ントリと EST 101,079 エントリの新規公開 <Event> DDBJ Hot Topics <Date> 2010-06-15 <Note>　マウス (Mus musculus) 胚 small RNA の MGA 397,593 エントリの新規公開 <Event> DDBJ Hot Topics <Date> 2010-04-02 <Note>　ゴマノハグサ科の一種 (Striga hermonthicas) EST 67,814エントリの 新規公開 <Event> DDBJ Hot Topics <Date> 2010-04-01 <Note>　イネ コシヒカリ (Oryza sativa Japonica Group, cultivar Koshihikari) WGS 654,543 エントリの新規公開 <Event> DDBJ Hot Topics <Date> 2010-04-01 <Note>　マウス (Mus musculus domesticus) GSS 122,131エントリの 新規公開 <Event> DDBJ Hot Topics <Date> 2010-03-03 <Note>　トマト (Solanum lycopersicum) GSS 93,682エントリの 新規公開 <Event> DDBJ Hot Topics <Date> 2010-02-16 <Note>　マウス (Mus musculus) MGA 84,606エントリの 新規公開 <Event> DDBJ Hot Topics <Date> 2010-02-04 <Note>　ブタ (Sus scrofa) EST 82,326エントリの新規公開 <Event> DDBJ Hot Topics <Date> 2010-01-07 <Note>　オキゴンド ウ （Pseudorca crassidens） GSS 90,007 エントリの新規公開 mail bulletin archive

Mail magazine
We will inform you of the thing commentary and the content of INSD when relating to the bank of http://www.ddbj.nig.ac.jp/ddbjnew/mag/monthly publication that the information team compiles.

<Event> DDBJ mail magazine No.56 <Date> 2010-12-22 <Note> DDBJ リリース 84.0 完成 /DDBJ 年 末年始休業のお知らせ /「DDBJing 講習会(23) ＆ PDBj 講習会 in 長浜」開催  /Sequin によるデータ登録受付終了のお知らせ /「ユー ザーの皆様へ，お願いです！」 ～その３．パーフェクトなデータ更新に向けて /"ＳＡＫＵＲＡ de Ｑ" 第８回 /DDBJ アノテータの業務紹介 ～１．Primary Database を維持するということ(後編 ) / <Event> DDBJ mail magazine No.55 <Date> 2010-12-01 <Note> 「DDBJing 講 習会(23) ＆ PDBj 講 習会 in 長浜」開催 /国 立遺伝学研究所の停電による公開サービスの停止 /DDBJ 年末年始休業のお 知らせ /DDBJ Sequence Read Archive より検索システムをリリース /RefSeq の BLAST Web API の公開 /ＳＡＫＵＲＡ 生物情報の入力方法が変更 /「ユーザーの皆様へ，お願いです！」 ～その２．よりスマートな公開のために /DDBJ アノテータの業務紹介 ～１．Primary Database を 維持するということ(前編) / <Event> DDBJ mail magazine No.54 <Date> 2010-11-01 <Note> 「DDBJing 講 習会 in 長浜」 開催 /初 の日本人全ゲノム配列データが DDBJ Sequence Read Archive か ら公開 /「完全長 cDNA 構 造解析プロジェクト」 由来の trace データを公開 /大量データの公開 /「ユー ザーの皆様へ，お願いです！」 ～その１．より迅速なアクセッション番号発行を目指して /DDBJ での特許関連配列データの公開業務の紹介（４） / <Event> DDBJ mail magazine No.53 <Date> 2010-09-30 <Note> 平成22年 度下期ＤＤＢＪオープンシステムプロジェクトの募集 /SAKURA でのテンプレートの削除について /DDBJ リ リース 83.0，DAD リ リース 53.0 完成 /DDBJ・DAD リリースならびに新着データの FASTA 形式変更 /DAD リリースにおける FASTA ファイル不具合のお詫び /SAKURA，DDBJing 講習会の「統合 TV」公開 /第23回国際実務者会議 報告 /DDBJ での特許関連配列データの公開業務の紹介(３） /"ＳＡＫＵＲＡ de Ｑ" 第７回 / <Event> DDBJ mail magazine No.52 <Date> 2010-09-01 <Note> BLAST での特許ア ミノ酸配列検索を追加 /NCBI RefSeq データのミラー公開 /"困った de Ｑ" 第２回 / <Event> DDBJ mail magazine No.51 <Date> 2010-07-29 <Note> DRA/ERA/SRA からの公開 データの提供を開始しました /AJACS & 第22回 DDBJing 講習会 終了 /DDBJ リリース 82.0, DAD リリース 52.0 完成 /DDBJ-XML 形式でのデータ提供終了のお知らせ /大量データの公開 /DDBJ で の特許関連配列データの公開業務の紹介（２） /"困った de Ｑ" 第１回 / <Event> DDBJ mail magazine No.50 <Date> 2010-05-27 <Note> AJACS & 第22回DDBJing 講習会 in 東京 開催 /次世代 シークエンサからの生データとアセンブルしたデータセットの公開 /getentry の 検索結果で画面に表示できない巨大エントリの結果取得方法の自動変更 /Twitter 始めました /DDBJ/EMBL/GenBank Feature Table Definition 改訂 /DAD リリース 51.0 完成 /大量データ の公開 /DDBJ での特許関連配列データの公開業務の紹介 /ＳＡＫＵＲＡ de "Ｑ" 第６回 / <Event> DDBJ mail magazine No.49 <Date> 2010-04-07 <Note> 「第22回 DDBJing 講習会 in 東京」 ライフサイエンス統合DBセンター共催 /UniProt のリリース番号とリリースサイクルが変更 /DDBJ リリース 81.0 完成 /日本特許庁および韓国特許庁アミノ酸配列データを Anonymous FTP にて公開 /大量データの公開 /検索・解析サービスの一部終了と変更のお知らせ /国立遺伝学研究所 大型計算機(supernig)利用申請 継続手続きのご案内 /「ＳＡＫＵＲＡ de "Ｑ" 」第５回 / <Event> DDBJ mail magazine No.48 <Date> 2010-03-04 <Note> 平成22年度上期ＤＤＢＪオープンシステムプロジェクトの募集 /共同研究会 「WABI か ら SABI へ」(生 物情報資源の相互運用性)開催のお知らせ /国立遺伝学研究所ならびに DDBJ ネットワークサービ ス，supernig 停止 / <Event> DDBJ mail magazine No.47 <Date> 2010-02-03 <Note> 検索・解析 サービスの一部終了のお知らせ /大量データの公開/Nucleic Acids Research に DDBJ に関する論文掲載 /DDBJ リ リース 80.0 完成 /DDBJ・EMBL・GenBank Feature Table Definition 改訂 /H-InvDB ミラーサイト公開終了のお知らせ /第9回 日韓中バイオインフォマティクストレーニングコース受講者募集 /「ＳＡＫＵＲＡ de "Ｑ"」第４回 /

担当チーム：情報 小平順子 鈴木紀美子 柳楽幸子 平田郁枝

For QA

 * The question concerning DDBJ was accepted on DDBJ HP so far. It has improved the efficiency of QA by will being to use question of opening to the public site "Life science QA" of the DBCLS sponsoring since November, 2010. If the question concerning the service of DDBJ is contributed, [anote-ta] of DDBJ is made to answer, too.

Inquiry of DDBJh life science QA
 * ttp://www.ddbj.nig.ac.jp/addresses-j.html
 * Question on DDBJ tag http://qa.lifesciencedb.jp/tags/ddbj/
 * Question on DRA tag http://qa.lifesciencedb.jp/tags/dra/

真島淳（構築チーム） 柳楽幸子（情報チーム）

HP management

 * The operational administrative of HP was made CMS at last and the homepage of CIB-DDBJ was updated in 2010. The homepage of DDBJ is shifting now, too.
 * http://cib-ddbj.genes.nig.ac.jp/en/

小菅武英（構築チーム） 鈴木紀美子（情報チーム） 渡邊茂樹

=COMMITTEE MEMBERS=
 * 1) <PERSON>城石俊彦<HASROLE>DNAデータ研究利用委員会委員委員長<PLACE>遺伝学研究所<YEAR>2010
 * 2) <PERSON>城石俊彦<HASROLE>系統生物研究センター長<PLACE>遺伝学研究所<YEAR>2010
 * 3) <PERSON>城石俊彦<HASROLE>国立遺伝学研究所系統生物研究センター長<PLACE>遺伝学研究所<YEAR>2010
 * 4) <PERSON>小笠原直毅<HASROLE>情報科学研究科教授<PLACE>奈良先端科学技術大学院大学<YEAR>2010
 * 5) <PERSON>小笠原直毅<HASROLE>DNAデータ研究利用委員会委員委員<PLACE>遺伝学研究所<YEAR>2010
 * 6) <PERSON>金久實<HASROLE>化学研究所教授<PLACE>京都大学<YEAR>2010
 * 7) <PERSON>金久實<HASROLE>DNAデータ研究利用委員会委員委員<PLACE>遺伝学研究所<YEAR>2010
 * 8) <PERSON>中村春木<HASROLE>蛋白質研究所教授<PLACE>大阪大学<YEAR>2010
 * 9) <PERSON>中村春木<HASROLE>DNAデータ研究利用委員会委員委員<PLACE>遺伝学研究所<YEAR>2010
 * 10) <PERSON>長村吉晃<HASROLE>基盤研究領域ゲノムリソースセンターセンター長<PLACE>（独）農業生物資源研究所<YEAR>2010
 * 11) <PERSON>長村吉晃<HASROLE>DNAデータ研究利用委員会委員委員<PLACE>遺伝学研究所<YEAR>2010
 * 12) <PERSON>服部正平<HASROLE>新領域創成科学研究科情報生命科学専攻・教授<PLACE>東京大学大学院<YEAR>2010
 * 13) <PERSON>服部正平<HASROLE>DNAデータ研究利用委員会委員委員<PLACE>遺伝学研究所<YEAR>2010
 * 14) <PERSON>菊池俊一<HASROLE>参事役（情報事業担当）<PLACE>(独)科学技術振興機構<YEAR>2010
 * 15) <PERSON>菊池俊一<HASROLE>DNAデータ研究利用委員会委員委員<PLACE>遺伝学研究所<YEAR>2010
 * 16) <PERSON>水島洋<HASROLE>疾患生命科学研究部教授<PLACE>東京医科歯科大学<YEAR>2010
 * 17) <PERSON>水島洋<HASROLE>DNAデータ研究利用委員会委員委員<PLACE>遺伝学研究所<YEAR>2010
 * 18) <PERSON>宮野悟<HASROLE>医科学研究所・ヒトゲノム解析センター教授<PLACE>東京大学<YEAR>2010
 * 19) <PERSON>宮野悟<HASROLE>DNAデータ研究利用委員会委員委員<PLACE>遺伝学研究所<YEAR>2010
 * 20) <PERSON>藤田信之<HASROLE>バイオテクノロジー本部次長<PLACE>（独）製品評価技術基盤機構<YEAR>2010
 * 21) <PERSON>藤田信之<HASROLE>DNAデータ研究利用委員会委員委員<PLACE>遺伝学研究所<YEAR>2010
 * 22) <PERSON>大久保公策<HASROLE>生命情報・DDBJ研究センター長・教授<PLACE>遺伝学研究所<YEAR>2010
 * 23) <PERSON>大久保公策<HASROLE>DNAデータ研究利用委員会委員委員<PLACE>遺伝学研究所<YEAR>2010
 * 24) <PERSON>五條堀孝<HASROLE>生命情報・DDBJ研究センター・教授<PLACE>遺伝学研究所<YEAR>2010
 * 25) <PERSON>五條堀孝<HASROLE>DNAデータ研究利用委員会委員委員<PLACE>遺伝学研究所<YEAR>2010
 * 26) <PERSON>中村保一<HASROLE>生命情報・DDBJ研究センター・教授<PLACE>遺伝学研究所<YEAR>2010
 * 27) <PERSON>中村保一<HASROLE>DNAデータ研究利用委員会委員委員<PLACE>遺伝学研究所<YEAR>2010
 * 28) <PERSON>斎藤成也<HASROLE>集団遺伝研究系・教授<PLACE>遺伝学研究所<YEAR>2010
 * 29) <PERSON>斎藤成也<HASROLE>DNAデータ研究利用委員会委員委員<PLACE>遺伝学研究所<YEAR>2010
 * 30) <PERSON>菅野純夫<HASROLE>新領域創成科学研究科教授<PLACE>東京大学大学院<YEAR>2010
 * 31) <PERSON>菅野純夫<HASROLE>国際諮問委員<PLACE>INSDCDDBJ<YEAR>2010
 * 32) <PERSON>中村春木<HASROLE>蛋白質研究所教授<PLACE>大阪大学<YEAR>2010
 * 33) <PERSON>中村春木<HASROLE>国際諮問委員<PLACE>INSDCDDBJ<YEAR>2010
 * 34) <PERSON>宮野悟<HASROLE>国際諮問委員<PLACE>INSDCDDBJ<YEAR>2010
 * 35) <PERSON>高木利久<HASROLE>生命情報・DDBJ研究センター・教授<PLACE>遺伝学研究所<YEAR>2010
 * 36) <PERSON>高木利久<HASROLE>新領域創成科学研究科教授<PLACE>東京大学大学院<YEAR>2010
 * 37) <PERSON>高木利久<HASROLE>DNAデータ研究利用委員会委員委員<PLACE>遺伝学研究所<YEAR>2010