JaponicusDB: rapid deployment of a model organism database for an emerging model species
Abstract The fission yeast Schizosaccharomyces japonicus has recently emerged as a powerful system for studying the evolution of essential cellular processes, drawing on similarities as well as key differences between S. japonicus and the related, well-established model Schizosaccharomyces pombe. We...
Saved in:
| Published in: | Genetics (Austin) Vol. 220; no. 4 |
|---|---|
| Main Authors: | , , , |
| Format: | Journal Article |
| Language: | English |
| Published: |
United States
Oxford University Press
04.04.2022
|
| Subjects: | |
| ISSN: | 1943-2631, 1943-2631 |
| Online Access: | Get full text |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| Abstract | Abstract
The fission yeast Schizosaccharomyces japonicus has recently emerged as a powerful system for studying the evolution of essential cellular processes, drawing on similarities as well as key differences between S. japonicus and the related, well-established model Schizosaccharomyces pombe. We have deployed the open-source, modular code and tools originally developed for PomBase, the S. pombe model organism database (MOD), to create JaponicusDB (www.japonicusdb.org), a new MOD dedicated to S. japonicus. By providing a central resource with ready access to a growing body of experimental data, ontology-based curation, seamless browsing and querying, and the ability to integrate new data with existing knowledge, JaponicusDB supports fission yeast biologists to a far greater extent than any other source of S. japonicus data. JaponicusDB thus enables S. japonicus researchers to realize the full potential of studying a newly emerging model species and illustrates the widely applicable power and utility of harnessing reusable PomBase code to build a comprehensive, community-maintainable repository of species-relevant knowledge. |
|---|---|
| AbstractList | Abstract
The fission yeast Schizosaccharomyces japonicus has recently emerged as a powerful system for studying the evolution of essential cellular processes, drawing on similarities as well as key differences between S. japonicus and the related, well-established model Schizosaccharomyces pombe. We have deployed the open-source, modular code and tools originally developed for PomBase, the S. pombe model organism database (MOD), to create JaponicusDB (www.japonicusdb.org), a new MOD dedicated to S. japonicus. By providing a central resource with ready access to a growing body of experimental data, ontology-based curation, seamless browsing and querying, and the ability to integrate new data with existing knowledge, JaponicusDB supports fission yeast biologists to a far greater extent than any other source of S. japonicus data. JaponicusDB thus enables S. japonicus researchers to realize the full potential of studying a newly emerging model species and illustrates the widely applicable power and utility of harnessing reusable PomBase code to build a comprehensive, community-maintainable repository of species-relevant knowledge. The fission yeast Schizosaccharomyces japonicus has recently emerged as a powerful system for studying the evolution of essential cellular processes, drawing on similarities as well as key differences between S. japonicus and the related, well-established model Schizosaccharomyces pombe. We have deployed the open-source, modular code and tools originally developed for PomBase, the S. pombe model organism database (MOD), to create JaponicusDB (www.japonicusdb.org), a new MOD dedicated to S. japonicus. By providing a central resource with ready access to a growing body of experimental data, ontology-based curation, seamless browsing and querying, and the ability to integrate new data with existing knowledge, JaponicusDB supports fission yeast biologists to a far greater extent than any other source of S. japonicus data. JaponicusDB thus enables S. japonicus researchers to realize the full potential of studying a newly emerging model species and illustrates the widely applicable power and utility of harnessing reusable PomBase code to build a comprehensive, community-maintainable repository of species-relevant knowledge. The fission yeast Schizosaccharomyces japonicus has recently emerged as a powerful system for studying the evolution of essential cellular processes, drawing on similarities as well as key differences between S. japonicus and the related, well-established model Schizosaccharomyces pombe. We have deployed the open-source, modular code and tools originally developed for PomBase, the S. pombe model organism database (MOD), to create JaponicusDB (www.japonicusdb.org), a new MOD dedicated to S. japonicus. By providing a central resource with ready access to a growing body of experimental data, ontology-based curation, seamless browsing and querying, and the ability to integrate new data with existing knowledge, JaponicusDB supports fission yeast biologists to a far greater extent than any other source of S. japonicus data. JaponicusDB thus enables S. japonicus researchers to realize the full potential of studying a newly emerging model species and illustrates the widely applicable power and utility of harnessing reusable PomBase code to build a comprehensive, community-maintainable repository of species-relevant knowledge.The fission yeast Schizosaccharomyces japonicus has recently emerged as a powerful system for studying the evolution of essential cellular processes, drawing on similarities as well as key differences between S. japonicus and the related, well-established model Schizosaccharomyces pombe. We have deployed the open-source, modular code and tools originally developed for PomBase, the S. pombe model organism database (MOD), to create JaponicusDB (www.japonicusdb.org), a new MOD dedicated to S. japonicus. By providing a central resource with ready access to a growing body of experimental data, ontology-based curation, seamless browsing and querying, and the ability to integrate new data with existing knowledge, JaponicusDB supports fission yeast biologists to a far greater extent than any other source of S. japonicus data. JaponicusDB thus enables S. japonicus researchers to realize the full potential of studying a newly emerging model species and illustrates the widely applicable power and utility of harnessing reusable PomBase code to build a comprehensive, community-maintainable repository of species-relevant knowledge. |
| Author | Oliferenko, Snezhana Rutherford, Kim M Harris, Midori A Wood, Valerie |
| Author_xml | – sequence: 1 givenname: Kim M surname: Rutherford fullname: Rutherford, Kim M organization: Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK – sequence: 2 givenname: Midori A orcidid: 0000-0003-4148-4606 surname: Harris fullname: Harris, Midori A organization: Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK – sequence: 3 givenname: Snezhana surname: Oliferenko fullname: Oliferenko, Snezhana email: snezhana.oliferenko@kcl.ac.uk organization: The Francis Crick Institute, London NW1 1AT, UK – sequence: 4 givenname: Valerie orcidid: 0000-0001-6330-7526 surname: Wood fullname: Wood, Valerie email: vw253@cam.ac.uk organization: Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/35380656$$D View this record in MEDLINE/PubMed |
| BookMark | eNpNkEtLxDAUhYOMOA_du5IsBamTxzRN3en4ZsCNgrtym96WSJvUpl3Mv3dkOuLqHDgfZ_HNycR5h4Scc3bNWSqXFTrsrQlLu4VcCHlEZjxdyUgoySf_-pTMQ_hijKk01idkKmOpmYrVjHy-QuudNUO4v7uhHbS2oAW2td826HrqSwq08QXW1HcVOBsaWkAPOQSkpe8oOIoNdpV11ciFFo3FcEqOS6gDno25IB-PD-_r52jz9vSyvt1EJhaqj7RKlVCrQsgETMKU4JjnWgkotcREpsiNTtAYjWDK0qySQiW5KQsNCliSKrkgl_vftvPfA4Y-a2wwWNfg0A8h250ngnPF-A69GNEhb7DI2s420G2zg40dcLUH_ND-rZxlv66zg-tsdC1_AGV3dPw |
| CitedBy_id | crossref_primary_10_1038_s41467_025_58515_w crossref_primary_10_3390_jof9050550 crossref_primary_10_1016_j_jbiosc_2022_07_014 crossref_primary_10_1002_yea_3912 crossref_primary_10_1002_yea_3919 crossref_primary_10_1093_genetics_iyad143 crossref_primary_10_1242_jcs_260568 crossref_primary_10_1093_g3journal_jkad028 crossref_primary_10_1093_genetics_iyac001 crossref_primary_10_1016_j_cub_2023_04_046 crossref_primary_10_1002_yea_3922 crossref_primary_10_1038_s41467_023_41347_x crossref_primary_10_1093_genetics_iyae007 crossref_primary_10_1002_yea_3930 |
| ContentType | Journal Article |
| Copyright | The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America. 2021 The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America. |
| Copyright_xml | – notice: The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America. 2021 – notice: The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America. |
| DBID | TOX CGR CUY CVF ECM EIF NPM 7X8 |
| DOI | 10.1093/genetics/iyab223 |
| DatabaseName | Oxford Journals Open Access Collection Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed MEDLINE - Academic |
| DatabaseTitle | MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) MEDLINE - Academic |
| DatabaseTitleList | MEDLINE MEDLINE - Academic |
| Database_xml | – sequence: 1 dbid: NPM name: PubMed url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 2 dbid: TOX name: Oxford Journals Open Access Collection url: https://academic.oup.com/journals/ sourceTypes: Publisher – sequence: 3 dbid: 7X8 name: MEDLINE - Academic url: https://search.proquest.com/medline sourceTypes: Aggregation Database |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Biology |
| EISSN | 1943-2631 |
| ExternalDocumentID | 35380656 10.1093/genetics/iyab223 |
| Genre | Research Support, Non-U.S. Gov't Journal Article |
| GrantInformation_xml | – fundername: Biotechnology and Biological Sciences Research Council grantid: BB/T000481/1 – fundername: Wellcome Trust grantid: 218236/Z/19/Z – fundername: NHGRI NIH HHS grantid: U24 HG012212 – fundername: Investigator Award in Science grantid: 220790/Z/20/Z – fundername: Cancer Research UK grantid: FC001002 – fundername: Wellcome Trust grantid: FC001002 |
| GroupedDBID | --- --Z -DZ -~X .-4 .55 .GJ 0R~ 186 18M 29H 2KS 2WC 34G 36B 39C 3V. 53G 5GY 5RE 5VS 5WD 7X2 7X7 85S 88A 88E 88I 8AO 8C1 8FE 8FH 8FI 8FJ 8G5 8R4 8R5 9M8 A8Z AABZA AACZT AAPXW AARHZ AASNB AAUAY AAUTI AAVAP AAYOK ABDNZ ABJNI ABMNT ABNHQ ABPPZ ABPTD ABTAH ABUWG ABXVV ACFRR ACGOD ACIHN ACIPB ACNCT ACPRK ACPVT ACUTJ ACYGS ADBBV ADIPN ADQBN ADVEK AEAQA AENEX AFFDN AFFNX AFFZL AFGWE AFKRA AFRAH AGMDO AHMBA AJEEA ALIPV ALMA_UNASSIGNED_HOLDINGS AOIJS APEBS ATCPS ATGXG AZQEC BAWUL BBNVY BCRHZ BENPR BES BEYMZ BHPHI BKNYI BKOMP BPHCQ BTFSW BVXVI C1A CCPQU CJ0 CS3 D0L DIK DU5 DWQXO E3Z EBD EBS EJD EMB EMOBN ESTFP F5P F8P F9R FD6 FLUFQ FOEOM FRP FYUFA GNUQQ GUQSH GX1 H13 HCIFZ HMCUK HYE H~9 INIJC K9- KBUDW KOP KQ8 KSI KSN L7B LK8 M0K M0L M0R M1P M2O M2P M7P MV1 MVM NHB NOMLY OBOKY OCZFY OHT OJZSN OK1 OMK OPAEJ OWPYF PQQKQ PROAC PSQYO Q2X QF4 QM4 QM9 QN7 QO4 R0Z RHF RHI ROX RPM RXW SJN SV3 TAE TGS TH9 TN5 TOX TR2 TWZ U5U UHB UKHRP UKR UNMZH UPT VQA W8F WH7 WHG WOQ X7M XOL XSW YHG YKV YSK YYP YYQ YZZ ZCA ZGI ZXP ZY4 ~KM ABDFA ABEJV ABGNP ABVGC ABXZS ADGKP AGORE AHGBF AHMMS AJBYB AJNCP ALXQX CGR CUY CVF ECM EIF JXSIZ NPM 7X8 ABUFD |
| ID | FETCH-LOGICAL-c526t-8696264d237ac70621ebb862af83e739e1c87ecc8eacffc47d67bcfd8a6a07963 |
| IEDL.DBID | TOX |
| ISICitedReferencesCount | 17 |
| ISICitedReferencesURI | http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=000756758000001&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| ISSN | 1943-2631 |
| IngestDate | Sun Nov 09 11:22:14 EST 2025 Sat May 31 02:10:54 EDT 2025 Wed Aug 28 03:17:30 EDT 2024 |
| IsDoiOpenAccess | true |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 4 |
| Keywords | annotation genome model organism database evolution curation Schizosaccharomyces japonicus |
| Language | English |
| License | This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America. |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c526t-8696264d237ac70621ebb862af83e739e1c87ecc8eacffc47d67bcfd8a6a07963 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
| ORCID | 0000-0001-6330-7526 0000-0003-4148-4606 |
| OpenAccessLink | https://dx.doi.org/10.1093/genetics/iyab223 |
| PMID | 35380656 |
| PQID | 2647211601 |
| PQPubID | 23479 |
| ParticipantIDs | proquest_miscellaneous_2647211601 pubmed_primary_35380656 oup_primary_10_1093_genetics_iyab223 |
| PublicationCentury | 2000 |
| PublicationDate | 2022-04-04 |
| PublicationDateYYYYMMDD | 2022-04-04 |
| PublicationDate_xml | – month: 04 year: 2022 text: 2022-04-04 day: 04 |
| PublicationDecade | 2020 |
| PublicationPlace | United States |
| PublicationPlace_xml | – name: United States |
| PublicationTitle | Genetics (Austin) |
| PublicationTitleAlternate | Genetics |
| PublicationYear | 2022 |
| Publisher | Oxford University Press |
| Publisher_xml | – name: Oxford University Press |
| SSID | ssj0006958 |
| Score | 2.4724777 |
| Snippet | Abstract
The fission yeast Schizosaccharomyces japonicus has recently emerged as a powerful system for studying the evolution of essential cellular processes,... The fission yeast Schizosaccharomyces japonicus has recently emerged as a powerful system for studying the evolution of essential cellular processes, drawing... |
| SourceID | proquest pubmed oup |
| SourceType | Aggregation Database Index Database Publisher |
| SubjectTerms | Databases, Factual Schizosaccharomyces - genetics |
| Title | JaponicusDB: rapid deployment of a model organism database for an emerging model species |
| URI | https://www.ncbi.nlm.nih.gov/pubmed/35380656 https://www.proquest.com/docview/2647211601 |
| Volume | 220 |
| WOSCitedRecordID | wos000756758000001&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| link | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV1LS8NAEB60KHjx_aiPskKvwW423d1481VEtPZQIbewr0APpqVphf57Z5O0B-1BLzmEzYOZyTwy-30D0Pbw4bBjo4BK50m1XRRoanWgrObO8q5juqTMfxX9vkySeFDzbBdrWvgxu0FBejxfcTNaKI3RDP0t7Upv08P3ZOV1edyVdRty3UU_8Gu_0sgynPT2_vUi-7BbZ43krlLzAWy4_BC2qzmSiyNIXtTEU9zOi8f7WzJVk5El1vlRvv7fHxlnRJFy5A2phjgVn8TvDPURjGDSSlROPE7Yzyuq13kAJtbQx_DRexo-PAf1yITAdEM-CySPsUKJbMiEMqLDQ-q0xqJFZZI5wWJHjRSoNYn-NstMJCwX2mRWKq46Aj_GE2jk49ydAaESF-H5SEkTRRHTQse4XIZGGyzyWBPaKNF0UpFipFUzm6VLIaW1kJpwvRR5ipbr2xEqd-N5kYaeuZ5SrAibcFrpYnU3hn4YkyN-_reHXMBO6GEJ5aaaS2jMpnN3BVvmazYqpi3YFInEY3_w1iqN5huj1cL5 |
| linkProvider | Oxford University Press |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=JaponicusDB%3A+rapid+deployment+of+a+model+organism+database+for+an+emerging+model+species&rft.jtitle=Genetics+%28Austin%29&rft.au=Rutherford%2C+Kim+M&rft.au=Harris%2C+Midori+A&rft.au=Oliferenko%2C+Snezhana&rft.au=Wood%2C+Valerie&rft.date=2022-04-04&rft.pub=Oxford+University+Press&rft.eissn=1943-2631&rft.volume=220&rft.issue=4&rft_id=info:doi/10.1093%2Fgenetics%2Fiyab223&rft.externalDocID=10.1093%2Fgenetics%2Fiyab223 |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1943-2631&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1943-2631&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1943-2631&client=summon |