Article Use Cases

Introduction

Below are sample use cases for the article objects found in the Fluidinfo eLife API.

Given a DOI, get all article values

Using the * wildcard for tag in a Fluidinfo query will get all values for an article object. The article object is located by a query on article/doi. In the example below, the DOI 10.7554/eLife.00013 is used.

Request

GET /values?query=elifesciences.org/api_v1/article/doi="10.7554/eLife.00013"&tag=*

Response

Status: 200 OK
Content-type: application/json
{
  "results": {
    "id": {
      "eb275979-d99d-4e44-a84f-15ce912ca888": {
        "fluiddb/about": {
          "username": "fluiddb",
          "updated-at": "2012-10-08T17:35:22.902590",
          "value": "http://dx.doi.org/10.7554/eLife.00013"
        },
        "elifesciences.org/api_v1/article/copyright_holder": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": "Alegado et al"
        },
        "elifesciences.org/api_v1/article/pub_date_day": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": 15
        },
        "elifesciences.org/api_v1/article/correspondence": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": "*For correspondence: jon_clardy@hms.harvard.edu (JC); nking@berkeley.edu (NK)"
        },
        "elifesciences.org/api_v1/article/pub_date_year": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": 2012
        },
        "elifesciences.org/api_v1/article/award_group_funding_source": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": "Gordon and Betty Moore Foundation Marine Microbiology Initiative"
        },
        "elifesciences.org/api_v1/article/research_organism": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": "Other"
        },
        "elifesciences.org/api_v1/article/license_url": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": "http://creativecommons.org/licenses/by/3.0/"
        },
        "elifesciences.org/api_v1/article/doi_url": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": "http://dx.doi.org/10.7554/eLife.00013"
        },
        "elifesciences.org/api_v1/article/author_notes": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": "†These authors contributed equally to this work."
        },
        "elifesciences.org/api_v1/article/ack": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": "AcknowledgementsWe thank Michael Fischbach, Richard Losick, and Russell Vance for critical reading of the manuscript. NK is a Fellow in the Integrated Microbial Biodiversity Program of the Canadian Institute for Advanced Research."
        },
        "elifesciences.org/api_v1/article/journal_title": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": "eLife"
        },
        "elifesciences.org/api_v1/article/keywords": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": [
            "Salpingoeca rosetta",
            "Algoriphagus",
            "bacterial sulfonolipid",
            "multicellular development"
          ]
        },
        "elifesciences.org/api_v1/article/authors": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": [
            "Rosanna A Alegado",
            "Laura W Brown",
            "Shugeng Cao",
            "Renee K Dermenjian",
            "Richard Zuzow",
            "Stephen R Fairclough",
            "Jon Clardy",
            "Nicole King"
          ]
        },
        "elifesciences.org/api_v1/article/award_group_award_id": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": "F32 GM086054"
        },
        "elifesciences.org/api_v1/article/accepted_date_day": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": 18
        },
        "elifesciences.org/api_v1/article/accepted_date_date": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": "July 18, 2012"
        },
        "elifesciences.org/api_v1/article/award_group_principle_award_recipient": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": "Nicole King"
        },
        "elifesciences.org/api_v1/article/article_title": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": "A bacterial sulfonolipid triggers multicellular development in the closest living relatives of animals"
        },
        "elifesciences.org/api_v1/article/refs": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": [
            "Agosta WC. 1992. Chemical communication. Scientific American Press , New York.",
            "Ahmed I Yokota A Fujiwara T. 2007. Chimaereicella boritolerans sp nov., a boron-tolerant and alkaliphilic bacterium of the family Flavobacteriaceae isolated from soil. Int J Syst Evol Microbiol 57: 986 – 992.",
            "Alegado RA Grabenstatter JD Zuzow R Morris A Huang SY Summons RE King N. 2012. Algoriphagus machipongonensis sp. nov. co-isolated with a colonial choanoflagellate. Int J Syst Evol Microbiol [epub ahead of print].",
            "An D Na C Bielawski J Hannun YA Kasper DL. 2011. Membrane sphingolipids as essential molecular signals for Bacteroides survival in the intestine. Proc Natl Acad Sci U S A 108 Suppl. 1: 4666 – 4671.",
            "Anton J Oren A Benlloch S Rodriguez-Valera F Amann R Rossello-Mora R. 2002. Salinibacter ruber gen. nov., sp nov., a novel, extremely halophilic member of the bacteria from saltern crystallizer ponds. Int J Syst Evol Microbiol 52: 485 – 491.",
            "Apicella MA. 2008. Isolation and characterization of lipopolysaccharides. Methods Mol Biol 431: 3 – 13.",
            "Atlas RM. 2004. Handbook of microbiological media , p. 2051. Boca Raton: CRC.",
            "Barbeyron T L’Haridon S Corre E Kloareg B Potin P. 2001. Zobellia galactanovorans gen. nov., sp. nov., a marine species of Flavobacteriaceae isolated from a red alga, and classification of [Cytophaga] uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Zobellia uliginosa gen. nov., comb. nov. Int J Syst Evol Microbiol 51 (Pt 3): 985 – 997.",
            "Bernardet J Segers P Vancanneyt M Berthe F Kersters K Vandamme P. 1996. Cutting a Gordian knot: Emended classification and description of the genus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom nov (basonym, Cytophaga aquatilis Strohl and Tait 1978). Int J Syst Bacteriol 46: 128 – 148.",
            "Blattner FR Plankett G III Bloch CA Perna N Burland V Riley M Collado-Vides J Glasner JD Rode CK Mayhew GF. 1997. The complete genome sequence of Escherichia coli K-12. Science 277: 1453 – 1462.",
            "Bligh EG Dyer WJ. 1959. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 37: 911 – 917.",
            "Bowman JP Nichols CM Gibson JAE. 2003. Algoriphagus ratkowskyi gen. nov., sp. nov., Brumimicrobium glaciale gen. nov., sp. nov., Cryomorpha ignava gen. nov., sp. nov. and Crocinitomix catalasitica gen. nov., sp. nov., novel flavobacteria isolated from various polar habitats. Int J Syst Evol Microbiol 53 (Pt 5): 1343 – 1355.",
            "Bradley RK Roberts A Smoot M Juvekar S Do J Dewey C Holmes I Pachter L. 2009. Fast statistical alignment. PLoS Comput Biol 5: e1000392.",
            "Brettar I Christen R Hofle M. 2004a. Aquiflexum balticum gen. nov., sp nov., a novel marine bacterium of the Cytophaga-Flavobacterium-Bacteroides group isolated from surface water of the central Baltic Sea. Int J Syst Evol Microbiol 54: 2335 – 2341.",
            "Brettar I Christen R Hofle MG. 2004b. Belliella baltica gen. nov., sp. nov., a novel marine bacterium of the Cytophaga-Flavobacterium-Bacteroides group isolated from surface water of the central Baltic Sea. Int J Syst Evol Microbiol 54 (Pt 1): 65 – 70.",
            "Burkholder PR Giles NH. 1947. Induced biochemical mutations in Bacillus subtilis. Am J Bot 34: 345 – 348.",
            "Butenandt A Beckmann R Hecker E. 1961. On the sex attractant of silk-moths. I. The biological test and the isolation of the pure sex-attractant bombykol. Hoppe-Seylers Z Physiol Chem 324: 71 – 83.",
            "Carlucci AF Pramer D. 1957. Factors influencing the plate method for determining abundance of bacteria in sea water. Proc Soc Exp Biol Med 96: 392 – 394.",
            "Carr M Leadbeater BSC Hassan R Nelson M Baldauf SL. 2008. Molecular phylogeny of choanoflagellates, the sister group to Metazoa. Proc Natl Acad Sci U S A 105: 16641 – 16646.",
            "Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17: 540 – 552.",
            "Cerdeno-Tarraga AM Patrick S Crossman L Blakely GW Abratt V Lennard N Poxton I Duerden B Harris B Quail MA. 2005. Extensive DNA inversions in the B. fragilis genome control variable gene expression. Blakely GW , editor. Science 307: 1463 – 1465.",
            "Chelius M Triplett E. 2000. Dyadobacter fermentans gen. nov., sp nov., a novel gram-negative bacterium isolated from surface-sterilized Zea mays stems. Int J Syst Evol Microbiol 50: 751 – 758.",
            "Cho J-C Giovannoni SJ. 2003. Croceibacter atlanticus gen. nov., sp. nov., a novel marine bacterium in the family Flavobacteriaceae. Syst Appl Microbiol 26: 76 – 83.",
            "Cho J-C Giovannoni SJ. 2004. Robiginitalea biformata gen. nov., sp. nov., a novel marine bacterium in the family Flavobacteriaceae with a higher G+C content. Int J Syst Evol Microbiol 54 (Pt 4): 1101 – 1106.",
            "Cohn ZA Morse SI. 1960. Functional and metabolic properties of polymorphonuclear leucocytes. II. The influence of a lipopolysaccharide endotoxin. J Exp Med 111: 689 – 704.",
            "Dayel MJ Alegado RA Fairclough SR Levin TC Nichols SA McDonald K King N. 2011. Cell differentiation and morphogenesis in the colony-forming choanoflagellate Salpingoeca rosetta. Dev Biol 357: 73 – 82.",
            "DeSantis TZ Hugenholtz P Larsen N Rojas M Brodie EL Keller K Huber T Dalevi D Hu P Andersen GL. 2006. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069 – 5072.",
            "Desbrosses GJ Stougaard J. 2011. Root nodulation: A paradigm for how plant-microbe symbiosis influences host developmental pathways. Cell Host Microbe 10: 348 – 358.",
            "Drijber R McGill W. 1994. Sulfonolipid content of Cytophaga and Flexibacter species isolated from soil and cultured under different nutrient and temperature regimes. Can J Microbiol 40: 132 – 139.",
            "Edman DC Pollock MB Hall ER. 1968. Listeria monocytogenes L forms. I. Induction maintenance, and biological characteristics. J Bacteriol 96: 352 – 357.",
            "Fairclough SR Dayel MJ King N. 2010. Multicellular development in a choanoflagellate. Curr Biol 20: R875 – R876.",
            "Falenstein J. 1989. PHYLIP—Phylogeny inference packages (version 3.2). Cladistics. 5: 164 – 166.",
            "Falke JJ Bass RB Butler SL Chervitz SA Danielson MA. 1997. The two-component signaling pathway of bacterial chemotaxis: A molecular view of signal transduction by receptors, kinases, and adaptation enzymes. Annu Rev Cell Dev Biol 13: 457 – 512.",
            "Falkow S. 2006. Is persistent bacterial infection good for your health? Cell 124: 699 – 702.",
            "Garrity GM. 2010. Bergey’s manual of systematic bacteriology: Bacteroidetes, spirochetes, tenericutes (mollicutes), acidobacteria, fibrobacteres, fusobacteria, dictyoglomi, gemmatimonadetes, lentisphaerae, verrucomicrobia, chlamydiae, and planctomycetes , p. 949. New York: Springer Verlag.",
            "Godchaux W Leadbetter ER. 1980. Capnocytophaga spp. contain sulfonolipids that are novel in procaryotes. J Bacteriol 144: 592 – 602.",
            "Godchaux W Leadbetter ER. 1983. Unusual sulfonolipids are characteristic of the Cytophaga-Flexibacter group. J Bacteriol 153: 1238 – 1246.",
            "Godchaux W Leadbetter ER. 1984. Sulfonolipids of gliding bacteria. Structure of the N-acylaminosulfonates. J Biol Chem 259: 2982 – 2990.",
            "Godchaux W Leadbetter E. 1988. Sulfonolipids are localized in the outer membrane of the gliding bacterium Cytophaga johnsonae. Arch Microbiol 150: 42 – 47.",
            "Hannich JT Umebayashi K Riezman H. 2011. Distribution and functions of sterols and sphingolipids. Cold Spring Harb Perspect Biol 3: pii: a004762. doi: 10.1101/cshperspect.a004762.",
            "Hannun YA Luberto C Argraves KM. 2001. Enzymes of sphingolipid metabolism: From modular to integrative signaling. Biochemistry 40: 4893 – 4903.",
            "Herr DR Fyrst H Phan V Heinecke K Georges R Harris GL Saba JD. 2003. Sply regulation of sphingolipid signaling molecules is essential for Drosophila development. Development 130: 2443 – 2453.",
            "Hibberd DJ. 1975. Observations on the ultrastructure of the choanoflagellate Codosiga botrytis (Ehr.) Saville-Kent with special reference to the flagellar apparatus. J Cell Sci 17: 191 – 219.",
            "Hoffmann JA Kafatos FC Janeway CA Ezekowitz RA. 1999. Phylogenetic perspectives in innate immunity. Science 284: 1313 – 1318.",
            "Hughes DT Sperandio V. 2008. Inter-kingdom signalling: Communication between bacteria and their hosts. Nat Rev Microbiol 6: 111 – 120.",
            "James-Clark H. 1867. On the spongiae ciliatae as infusoria flagellata; or observations on the structure, animality, and relationship of Leucosolenia botryoides, Bowerbank. Memoirs Boston Soc. Of Nat. Hist. I, two plates.",
            "de Jonge BL Chang YS Gage D Tomasz A. 1992. Peptidoglycan composition in heterogeneous Tn551 mutants of a methicillin-resistant Staphylococcus aureus strain. J Biol Chem 267: 11255 – 11259.",
            "Kamiyama T Umino T Itezono Y Nakamura Y Satoh T Yokose K. 1995a. Sulfobacins A and B, novel von Willebrand factor receptor antagonists. II. Structural elucidation. J Antibiot 48: 929 – 936.",
            "Kamiyama T Umino T Satoh T Sawairi S Shirane M Ohshima S Yokose K. 1995b. Sulfobacins A and B, novel von Willebrand factor receptor antagonists. I. Production, isolation, characterization and biological activities. J. Antibiot 48: 924 – 928.",
            "Karpov SA Coupe SJ. 1998. A revision of choanoflagellate genera Kentrosiga, Schiller, 1953 and Desmarella, Kent, 1880. Acta Protozoologica 37: 23 – 27.",
            "Kimbrell DA Beutler B. 2001. The evolution and genetics of innate immunity. Nat Rev Genet 2: 256 – 267.",
            "King N. 2004. The unicellular ancestry of animal development. Dev Cell 7: 313 – 325.",
            "King N Carroll SB. 2001. A receptor tyrosine kinase from choanoflagellates: Molecular insights into early animal evolution. Proc Natl Acad Sci U S A 98: 15032 – 15037.",
            "King N Hittinger CT Carroll SB. 2003. Evolution of key cell signaling and adhesion protein families predates animal origins. Science 301: 361 – 363.",
            "King N Westbrook MJ Young SL Kuo A Abedin M Chapman J Fairclough S Hellsten U Isogai Y. 2008. The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature 451: 783 – 788.",
            "King N Young SL Abedin M Carr M Leadbeater BSC. 2009. Starting and maintaining Monosiga brevicollis cultures. Cold Spring Harb Protoc. 2009: pdb.prot5148.",
            "Kobayashi J Mikami S Shigemori H Takao TYS Izuta S Yoshida S. 1995. Flavocristamides A and B, new DNA polymerase α inhibitors from a marine bacterium sp. Tetrahedron 51: 10487 – 10490.",
            "Kopp EB Medzhitov R. 1999. The Toll-receptor family and control of innate immunity. Curr Opin Immunol 11: 13 – 18.",
            "Koropatnick TA Engle JT Apicella MA Stabb EV Goldman WE Mcfall-Ngai MJ. 2004. Microbial factor-mediated development in a host-bacterial mutualism. Science 306: 1186 – 1188.",
            "Kreft JM. 2010. Effects of forming multicellular colonies or attaching to surfaces on feeding rates of the choanoflagellate Salpingoeca rosetta. Koehl M , editor. Thesis (M.A. in Integrative Biology). University of California , Berkeley.",
            "Kunst F Ogasawara N Moszer I Albertini AM Alloni G Azevedo V Bertero MG Bessières P Bolotin A Borchert S. 1997. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390: 249 – 256.",
            "Leadbeater BSC. 1983. Life-history and ultrastructure of a new marine species of Proterospongia (Choanoflagellida). J Mar Biol Assoc UK 63: 135 – 160.",
            "Lee YK Mazmanian SK. 2010. Has the microbiota played a critical role in the evolution of the adaptive immune system? Science 330: 1768 – 1773.",
            "Lewin R. 1969. A classification of flexibacteria. J Gen Microbiol 58: 189 – 206.",
            "Matsunaga T Okamura Y Fukuda Y Wahyudi AT Murase Y Takeyama H. 2005. Complete genome sequence of the facultative anaerobic magnetotactic bacterium Magnetospirillum sp. strain AMB-1. DNA Res 12: 157 – 166.",
            "Matsuo Y Suzuki M Kasai H Shizuri Y Harayama S. 2003. Isolation and phylogenetic characterization of bacteria capable of inducing differentiation in the green alga Monostroma oxyspermum. Environ Microbiol 5: 25 – 35.",
            "Matsuo Y Imagawa H Nishizawa M Shizuri Y. 2005. Isolation of an algal morphogenesis inducer from a marine bacterium. Science 307: 1598.",
            "Mazmanian SK Liu CH Tzianabos AO Kasper DL. 2005. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 122: 107 – 118.",
            "Mazmanian SK Round JL Kasper DL. 2008. A microbial symbiosis factor prevents intestinal inflammatory disease. Nature 453: 620 – 625.",
            "McFall-Ngai M. 1999. Consequences of evolving with bacterial symbionts: Insights from the squid-vibrio associations. Ann Rev Ecol Syst 30: 235 – 256.",
            "Medzhitov R Janeway C. 2000. Innate immune recognition: Mechanisms and pathways. Immunol Rev 173: 89 – 97.",
            "Merrill AH Sullards MC Wang E Voss KA Riley RT. 2001. Sphingolipid metabolism: Roles in signal transduction and disruption by fumonisins. Environ Health Perspect 109 Suppl. 2: 283 – 289.",
            "Miller TR Delcher AL Salzberg SL Saunders E Detter JC Halden RU. 2010. Genome sequence of the dioxin-mineralizing bacterium Sphingomonas wittichii RW1. J Bacteriol 192: 6101 – 6102.",
            "Møller JD Barnes AC Dalsgaard I Ellis AE. 2005. Characterisation of surface blebbing and membrane vesicles produced by Flavobacterium psychrophilum. Dis Aquat Organ 64: 201 – 209.",
            "Nedashkovskaya OI Vancanneyt M Van Trappen S Vandemeulebroecke K Lysenko AM Rohde M Falsen E Frolova GM Mikhailov VV Swings J. 2004. Description of Algoriphagus aquimarinus sp. nov., Algoriphagus chordae sp. nov. and Algoriphagus winogradskyi sp. nov., from sea water and algae, transfer of Hongiella halophila Yi and Chun 2004 to the genus Algoriphagus as Algoriphagus halophilus comb. nov. and emended descriptions of the genera Algoriphagus Bowman,. 2003 and Hongiella Yi and Chun 2004. Int J Syst Evol Microbiol 54 (Pt 5): 1757 – 1764.",
            "Nedashkovskaya O Kim S Vancanneyt M Lysenko A Shin D Park M Lee KH Jung WJ Kalinovskaya NI Mikhailov VV. 2006. Echinicola pacifica gen. nov., sp nov., a novel flexibacterium isolated from the sea urchin Strongylocentrotus intermedius. Int J Syst Evol Microbiol 56: 953 – 958.",
            "Nierman WC Feldblyum TV Laub MT Paulsen IT Nelson KE Eisen JA Heidelberg JF Alley MR Ohta N Maddock JR. 2001. Complete genome sequence of Caulobacter crescentus. Proc Natl Acad Sci U S A 98: 4136 – 4141.",
            "Oh H-M Kang I Yang S-J Jang Y Vergin KL Giovannoni SJ Cho JC. 2011. Complete genome sequence of strain HTCC2170, a novel member of the genus Maribacter in the family Flavobacteriaceae. J Bacteriol 193: 303 – 304.",
            "Olsen I Jantzen E. 2001. Sphingolipids in bacteria and fungi. Anaerobe 7: 103 – 112.",
            "Prieschl EE Baumruker T. 2000. Sphingolipids: Second messengers, mediators and raft constituents in signaling. Immunol Today 21: 555 – 560.",
            "Provasoli L Pintner I. 1980. Bacteria induced polymorphism in an axenic laboratory strain of Ulva lactuca (Chlorophyceae). J Phycol 16: 196 – 201.",
            "Pyne S Pyne NJ. 2000. Sphingosine 1-phosphate signalling in mammalian cells. Biochem J 349 (Pt 2): 385 – 402.",
            "Raj H Maloy S. 1990. Proposal of Cyclobacterium-Marinus gen-nov, comb-nov for a marine bacterium previously assigned to the genus Flectobacillus. Int J Syst Bacteriol 40: 337 – 347.",
            "Roelofs WL. 1995. Chemistry of sex attraction. Proc Natl Acad Sci U S A 92: 44 – 49.",
            "Ruby EG Urbanowski M Campbell J Dunn A Faini M Gunsalus R Lostroh P Lupp C McCann J Millikan D. 2005. Complete genome sequence of Vibrio fischeri: A symbiotic bacterium with pathogenic congeners. Proc Natl Acad Sci U S A 102: 3004 – 3009.",
            "Ruiz-Trillo I Roger AJ Burger G Gray MW Lang BF. 2008. A phylogenomic investigation into the origin of metazoa. Mol Biol Evol 25: 664 – 672.",
            "Saville Kent W. 1880. A manual of the infusoria. David Bogue , London.",
            "Schaefer AL Hanzelka BL Eberhard A Greenberg EP. 1996. Quorum sensing in Vibrio fischeri: Probing autoinducer-LuxR interactions with autoinducer analogs. J Bacteriol 178: 2897 – 2901.",
            "Spiegel S Milstien S. 2000. Sphingosine-1-phosphate: Signaling inside and out. FEBS Lett 476: 55 – 57.",
            "Spizizen J. 1958. Transformation of biochemically deficient strains of Bacillus subtilis by deoxyribonucleate. Proc Natl Acad Sci USA 44: 1072 – 1078.",
            "Takeuchi O Hoshino K Kawai T Sanjo H Takada H Ogawa T Takeda K Akira S. 1999. Differential roles of TLR2 and TLR4 in recognition of gram-negative and gram-positive bacterial cell wall components. Immunity 11: 443 – 451.",
            "Talavera G Castresana J. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 56: 564 – 577.",
            "Tiago I Mendes V Pires C Morais PV Veríssimo A. 2006. Chimaereicella alkaliphila gen. nov., sp. nov., a Gram-negative alkaliphilic bacterium isolated from a nonsaline alkaline groundwater. Syst Appl Microbiol 29: 100 – 108.",
            "Van Trappen S Vandecandelaere I Mergaert J Swings J. 2004. Algoriphagus antarcticus sp. nov., a novel psychrophile from microbial mats in Antarctic lakes. Int J Syst Evol Microbiol 54 (Pt 6): 1969 – 1973.",
            "Webster NS Smith LD Heyward AJ Watts JEM Webb RI Blackall LL Negri AP. 2004. Metamorphosis of a scleractinian coral in response to microbial biofilms. Appl Environ Microbiol 70: 1213 – 1221.",
            "Weisburg WG Barns SM Pelletier DA Lane DJ. 1991. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173: 697 – 703.",
            "Wexler HM. 2007. Bacteroides: The good, the bad, and the nitty-gritty. Clin Microbiol Rev 20: 593 – 621.",
            "Wood DW Setubal JC Kaul R Monks DE Kitajima JP Okura VK Zhou Y Chen L Wood GE Almeida NF Jr. 2001. The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science 294: 2317 – 2323.",
            "Yi H Chun J. 2004. Hongiella mannitolivorans gen. nov., sp. nov., Hongiella halophila sp. nov. and Hongiella ornithinivorans sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 54 (Pt 1): 157 – 162.",
            "Yoon J-H Yeo S-H Oh TK. 2004. Hongiella marincola sp. nov., isolated from sea water of the East Sea in Korea. Int J Syst Evol Microbiol 54 (Pt 5): 1845 – 1848.",
            "Yoon J-H Kang S-J Oh TK. 2005a. Algoriphagus locisalis sp. nov., isolated from a marine solar saltern. Int J Syst Evol Microbiol 55 (Pt 4): 1635 – 1639.",
            "Yoon J-H Kang S-J Jung S-Y Lee C-H Oh TK. 2005b. Algoriphagus yeomjeoni sp. nov., isolated from a marine solar saltern in the Yellow Sea, Korea. Int J Syst Evol Microbiol 55 (Pt 2): 865 – 870.",
            "Yoon J-H Lee M-H Kang S-J Oh TK. 2006. Algoriphagus terrigena sp. nov., isolated from soil. Int J Syst Evol Microbiol 56 (Pt 4): 777 – 780.",
            "Zhou L Srisatjaluk R Justus DE Doyle RJ. 1998. On the origin of membrane vesicles in gram-negative bacteria. FEMS Microbiol Lett 163: 223 – 228.",
            "Ziegler TA Forward RB. 2007. Larval release behaviors in the Caribbean spiny lobster, Panulirus argus: Role of peptide pheromones. J Chem Ecol 33: 1795 – 1805."
          ]
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        "elifesciences.org/api_v1/article/conflict": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": "The remaining authors have no competing interests to declare."
        },
        "elifesciences.org/api_v1/article/funding_statement": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": "The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication."
        },
        "elifesciences.org/api_v1/article/publisher": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": "eLife Sciences Publications, Ltd"
        },
        "elifesciences.org/api_v1/article/received_date_date": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": "May 22, 2012"
        },
        "elifesciences.org/api_v1/article/accepted_date_timestamp": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": 1342569600
        },
        "elifesciences.org/api_v1/article/abstract": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": "Bacterially-produced small molecules exert profound influences on animal health, morphogenesis, and evolution through poorly understood mechanisms. In one of the closest living relatives of animals, the choanoflagellate Salpingoeca rosetta, we find that rosette colony development is induced by the prey bacterium Algoriphagus machipongonensis and its close relatives in the Bacteroidetes phylum. Here we show that a rosette inducing factor (RIF-1) produced by A. machipongonensis belongs to the small class of sulfonolipids, obscure relatives of the better known sphingolipids that play important roles in signal transmission in plants, animals, and fungi. RIF-1 has extraordinary potency (femtomolar, or 10−15 M) and S. rosetta can respond to it over a broad dynamic range—nine orders of magnitude. This study provides a prototypical example of bacterial sulfonolipids triggering eukaryotic morphogenesis and suggests molecular mechanisms through which bacteria may have contributed to the evolution of animals."
        },
        "elifesciences.org/api_v1/article/license": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": "This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited."
        },
        "elifesciences.org/api_v1/article/accepted_date_year": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": 2012
        },
        "elifesciences.org/api_v1/article/doi": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": "10.7554/eLife.00013"
        },
        "elifesciences.org/api_v1/article/license_type": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": "open-access"
        },
        "elifesciences.org/api_v1/article/accepted_date_month": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": 7
        },
        "elifesciences.org/api_v1/article/journal_issn_epub": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": "2050-084X"
        },
        "elifesciences.org/api_v1/article/copyright_year": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": 2012
        },
        "elifesciences.org/api_v1/article/copyright_statement": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": "Copyright © 2012, Alegado et al"
        },
        "elifesciences.org/api_v1/article/pub_date_month": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": 10
        },
        "elifesciences.org/api_v1/article/journal_id": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": "elife"
        },
        "elifesciences.org/api_v1/article/components": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": [
            "http://dx.doi.org/10.7554/eLife.00013.001",
            "http://dx.doi.org/10.7554/eLife.00013.002",
            "http://dx.doi.org/10.7554/eLife.00013.003",
            "http://dx.doi.org/10.7554/eLife.00013.004",
            "http://dx.doi.org/10.7554/eLife.00013.005",
            "http://dx.doi.org/10.7554/eLife.00013.006",
            "http://dx.doi.org/10.7554/eLife.00013.007",
            "http://dx.doi.org/10.7554/eLife.00013.008",
            "http://dx.doi.org/10.7554/eLife.00013.009",
            "http://dx.doi.org/10.7554/eLife.00013.010",
            "http://dx.doi.org/10.7554/eLife.00013.011",
            "http://dx.doi.org/10.7554/eLife.00013.012",
            "http://dx.doi.org/10.7554/eLife.00013.013",
            "http://dx.doi.org/10.7554/eLife.00013.014",
            "http://dx.doi.org/10.7554/eLife.00013.015",
            "http://dx.doi.org/10.7554/eLife.00013.016",
            "http://dx.doi.org/10.7554/eLife.00013.017",
            "http://dx.doi.org/10.7554/eLife.00013.018",
            "http://dx.doi.org/10.7554/eLife.00013.019",
            "http://dx.doi.org/10.7554/eLife.00013.020",
            "http://dx.doi.org/10.7554/eLife.00013.021",
            "http://dx.doi.org/10.7554/eLife.00013.022",
            "http://dx.doi.org/10.7554/eLife.00013.023",
            "http://dx.doi.org/10.7554/eLife.00013.024",
            "http://dx.doi.org/10.7554/eLife.00013.025",
            "http://dx.doi.org/10.7554/eLife.00013.026",
            "http://dx.doi.org/10.7554/eLife.00013.027",
            "http://dx.doi.org/10.7554/eLife.00013.028",
            "http://dx.doi.org/10.7554/eLife.00013.029",
            "http://dx.doi.org/10.7554/eLife.00013.030"
          ]
        },
        "elifesciences.org/api_v1/article/subject_area": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": [
            "Research article",
            "Cell biology"
          ]
        },
        "elifesciences.org/api_v1/article/received_date_timestamp": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": 1337644800
        },
        "elifesciences.org/api_v1/article/pub_date_date": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-27T01:00:03.785279",
          "value": "October 15, 2012"
        }
      }
    }
  }
}

Given a month, get all articles published that month

In this example, instead of a * wildcard for tag, it will only get the article DOI. To filter objects by date of publication, and specifically for the month of October 2012, the query string will search by article/pub_date_month = 10 and article/pub_date_year = 2012. Numeric value matching is possible on these tags, since the data stored is integer type.

Request

GET /values?query=elifesciences.org/api_v1/article/pub_date_month=10 and elifesciences.org/api_v1/article/pub_date_year=2012&tag=elifesciences.org/api_v1/article/doi

Response

Status: 200 OK
Content-type: application/json
{
  "results": {
    "id": {
      "eb275979-d99d-4e44-a84f-15ce912ca888": {
        "elifesciences.org/api_v1/article/doi": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-23T23:10:22.321767",
          "value": "10.7554/eLife.00013"
        }
      },
      "82aba95e-100e-468a-b5c4-4457ae69d215": {
        "elifesciences.org/api_v1/article/doi": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-23T23:12:04.696060",
          "value": "10.7554/eLife.00048"
        }
      },
      "fd6804e2-70be-4ced-a896-9e153bacada7": {
        "elifesciences.org/api_v1/article/doi": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-23T23:08:30.035787",
          "value": "10.7554/eLife.00007"
        }
      },
      "55decf52-a0d9-42d2-8db9-d5924a40a57a": {
        "elifesciences.org/api_v1/article/doi": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-23T23:19:30.156722",
          "value": "10.7554/eLife.00243"
        }
      },
      "71e9f5be-56a1-4e5a-a04a-35d2cfc75145": {
        "elifesciences.org/api_v1/article/doi": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-23T23:18:11.840778",
          "value": "10.7554/eLife.00240"
        }
      },
      "b55573b5-d12a-4604-b7eb-5f06ff1a94ef": {
        "elifesciences.org/api_v1/article/doi": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-23T23:19:03.118978",
          "value": "10.7554/eLife.00242"
        }
      },
      "749f6115-0848-4f59-9b52-adbc461c8ced": {
        "elifesciences.org/api_v1/article/doi": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-23T23:21:07.267530",
          "value": "10.7554/eLife.00286"
        }
      },
      "337aa9e5-0c48-422b-945a-be12353f6fe2": {
        "elifesciences.org/api_v1/article/doi": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-23T23:12:52.581687",
          "value": "10.7554/eLife.00065"
        }
      },
      "0c0e0ea4-1530-441a-bb97-9d26ebf65647": {
        "elifesciences.org/api_v1/article/doi": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-23T23:20:58.570089",
          "value": "10.7554/eLife.00270"
        }
      }
    }
  }
}

Given a subject area, get all articles in that subject area

This example uses the “contains” operator in the Fluidinfo query to case sensitive match a list value. In this case, it is matching “Cell biology” in an article/subject_area list.

Request

GET /values?query=elifesciences.org/api_v1/article/subject_area contains "Cell biology"&tag=elifesciences.org/api_v1/article/doi

Response

Status: 200 OK
Content-type: application/json
{
  "results": {
    "id": {
      "eb275979-d99d-4e44-a84f-15ce912ca888": {
        "elifesciences.org/api_v1/article/doi": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-23T23:10:22.321767",
          "value": "10.7554/eLife.00013"
        }
      },
      "55decf52-a0d9-42d2-8db9-d5924a40a57a": {
        "elifesciences.org/api_v1/article/doi": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-23T23:19:30.156722",
          "value": "10.7554/eLife.00243"
        }
      },
      "b55573b5-d12a-4604-b7eb-5f06ff1a94ef": {
        "elifesciences.org/api_v1/article/doi": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-23T23:19:03.118978",
          "value": "10.7554/eLife.00242"
        }
      },
      "82aba95e-100e-468a-b5c4-4457ae69d215": {
        "elifesciences.org/api_v1/article/doi": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-23T23:12:04.696060",
          "value": "10.7554/eLife.00048"
        }
      }
    }
  }
}

Given a keyword, search articles with matching title or abstract

This example uses the “matches” operator in the Fluidinfo query to case insensitive match full words. In this case, the keyword can match in the article/article_title or the article/abstract.

Request

GET /values?query=elifesciences.org/api_v1/article/article_title matches "hormone" or elifesciences.org/api_v1/article/abstract matches "hormone"&tag=elifesciences.org/api_v1/article/doi

Response

Status: 200 OK
Content-type: application/json
{
  "results": {
    "id": {
      "749f6115-0848-4f59-9b52-adbc461c8ced": {
        "elifesciences.org/api_v1/article/doi": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-23T23:21:07.267530",
          "value": "10.7554/eLife.00286"
        }
      },
      "337aa9e5-0c48-422b-945a-be12353f6fe2": {
        "elifesciences.org/api_v1/article/doi": {
          "username": "elifesciences.org",
          "updated-at": "2012-10-23T23:12:52.581687",
          "value": "10.7554/eLife.00065"
        }
      }
    }
  }
}
 

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Subject to a Creative Commons Attribution license, except where otherwise noted.