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Arctos is a museum collections management system
https://arctos.database.museum
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"unknown" publications #1570

Closed dustymc closed 2 years ago

dustymc commented 6 years ago

Suggest we clean up or delete these publications which contain "unknown" or use agent unknown.

 begin
    for r in (
      select publication.publication_id,full_citation from publication where lower(full_citation) like '%unknown%'
      union 
      select publication.publication_id,full_citation from publication,publication_agent where publication.publication_id=publication_agent.publication_id and agent_id=0
    ) loop
    dbms_output.put_line(r.full_citation);
    for c in (
      select guid_prefix,count(*) cnt from citation, cataloged_item,collection
      where citation.collection_object_id=cataloged_item.collection_object_id and
      cataloged_item.collection_id=collection.collection_id and
      citation.publication_id=r.publication_id
      group by guid_prefix
    ) loop
      dbms_output.put_line('    - ' || c.guid_prefix || ' @ ' || c.cnt);
    end loop;
  end loop;
end;
 19  /

unknown. 2000. Lake Baikal: A mirror in time and space for understanding global change processes.
unknown. 1997. Molecular genetics of marine mammals.
unknown. 2002. Encyclopedia of marine mammals.
unknown. 2002. Otter Conservation- An Example for a Sustainable Use of Wetlands.
unknown. 2005. Ariteus flavescens. Mammalian Species 900(1):1-5.
unknown. 2003. Implications of ITS sequences and RAPD markers for the taxonomy and biogeography of the <i>Oxytropis campestris</i> and <i>O. arctica</i> (Fabacae) complexes in Alaska. American Journal of Botany 90(10):1470-1480.
unknown. 1942. Flora and Alaska and Yukon. Acta Universitatis Lundensis, n.s. 38:257-257.
unknown. 2007. Parrya nauruaq (Brassicaceae). a new species from Alaska. Novon 17:275-278.
unknown. 2005. Mammalian Diversification:  From Chromosomes to Phylogeny.
unknown. . in prep. (Nototriton limnospectator). unknown:-.
unknown. 1992. Gopher snake attraction to bird's nests. Southwestern Naturalist 37(3):293-298.
unknown. 1993. Arboreal sprint failure: lizardfall in a California woodland. Ecology 74(8):2465-2467.
unknown. 1983. Homerange in the western fence lizard (Sceloporus occidentalis occidentalis). Copeia 1983(4):933-940.
unknown. 1967. Growth and size of the western fence lizard (Sceloporus occidentalis). Copeia 1967(4):721-731.
unknown. 1980. The times of mating and oviposition of the western fence lizard, Sceloporus occidentalis occidentalis. Journal of Herpetology 14(1):102-102.
unknown. 1972. Habitat preferences and the distribution of Uta stansburiana and Sceloperous occidentalis in coastal California. Copeia 1972(4):643-649.
unknown. 1997. Taricha torosa (California newt) response to fire. Herpetological Review 28(2):82-83.
unknown. 1994. The status of the California tiger salamander (Ambystoma californiense) at Lagunita: A 50 year update. Journal of Herpetology 28(2):159-164.
unknown. 1998. Demography, migration, and metapopulation structure of pond breeding salamanders.
unknown. 1962. Homing in the California vole, Microtus californicus. American Midland Naturalist 68(2):357-368.
unknown. 1967. Some effects of deer browsing on chamise sprouts after fire. American Midland Naturalist 77(1):234-238.
unknown. 1981. An experimental examination of an artificial dispersal sink. Journal of Mammalogy 62(1):74-81.
unknown. 1975. The effects of an artificial water supply on free-living Peromyscus truei. Journal of Mammalogy 56:705-707.
unknown. 1967. The internal anatomy of home range. Journal of Mammalogy 48(4):529-536.
unknown. 1965. The adrenal cortex and its hormones in the California ground squirrel, Spermophilus beecheyi. Journal of Mammalogy 46(3):446-450.
unknown. 1992. Dispersal in the monogamous rodent rodent, <i>Peromyscus californicus</i>. Ecology 73(3):859-866.
unknown. 1974. Water stress of free-living Peromyscus truei. Ecology 55:1407-1414.
unknown. 1979. An experimental study of dispersal in the California ground squirrel. Ecology 60(6):1103-1109.
unknown. 1962. The use of water as bait for Microtus californicus. Journal of Mammalogy 43(4):555-556.
unknown. 1966. Homing in the western harvest mouse, Reithrodontomys megalotis. Journal of Mammalogy 47(1):53-58.
unknown. 1967. An experimental analysis of orientation to the homesite in two rodent species. Canadian Journal of Zoology 45:261-268.
unknown. 1946. The California ground squirrel: A record of observations made on the Hastings Natural History Reservation. 475pp.
unknown. 1979. Geographic variation in genic and morphological characters in Peromyscus californicus. Journal of Mammalogy 60(4):705-722.
unknown. 1990. Social organization and nest co-occupancy in Peromyscus californicus, a monogamous rodent. Behavioral Ecology and Sociobiology 26:9-15.
unknown. 1984. Seasonal aggression independent of seasonal testosterone in wood rats. Proceedings of The National Academy of Science 81:5255-5257.
unknown. 1996. Genetic variation and immune response in natural populations of pocket gophers. Conservation Biology 10(6):1519-1527.
unknown. 1991. The monogamous mating system of Peromyscus californicus as revealed by DNA fingerprinting. Behavioral Ecology and Sociobiology 29:161-166.
unknown. 1996. Long term patterns in coastal California grasslands in relation to cultivation, gophers, and grazing. Ecological Applications 64(4):1189-1211.
unknown. 1981. Relationships between genetic variability and niche dimensions among coexisting species of Peromyscus. Journal of Mammalogy 62(2):273-285.
unknown. 1997. Population dynamics of small mammals in an oak woodland-grassland-chaparral habitat mosaic. Southwestern Naturalist 42(1):1-12.
unknown. 1943. Work with vertebrate animals on the Hastings Natural History Reservation. American Midland Naturalist 30:254-267.
unknown. 1974. Distribution and habitat preferences of the amphibians and reptiles of Hastings Natural History Reservation. 30pp.
unknown. . Current Topics in Microbiology and Immunology.
unknown. 2004. Phylogeny and Divergence-Date Estimates of Rapid Radiations in Muroid Rodents Based on Multiple Nuclear Genes. Systematic Biology 53(4):533-553.
unknown. 1978. Evolutionary Relationships of Kangaroo Mice, Genus Microdipodops. Journal of Mammalogy 59(2):354-365.
unknown. 2008. Phylogeography and species boundaries of the western North American Nightsnake (Hypsiglena torquata): Revisiting the subspecies concept. Molecular Phylogenetics and Evolution 46:1095-1115.
Gabor R. Racz and William L. Gannon. 2005. Improving collection maintenance through innovation: bar-code labeling to track specimens in the processing stream. unknown 1:227-241.
Luis A. Ruedas and Elder. 1994. On the putative existence of a diploid number 42 cytotype of <i>Sylvilagus aquaticus</i> (Bachman, 1837: Lagomorpha: Leporidae). Mammalia 58:250-253.
Dr. Carol W. Allison. 1973. Late Proterozoic Tindir Group, Alaska      . unknown unknown(unknown):65-68.
Brian Hjelle and Fernando Torres-Perez. 2010. Hantaviruses in the Americas and Their Role as Emerging Pathogens. unknown 2:2559-2586.
Terry L. Yates and James Estes. 1991. Support for Biodiversity research at the National Science Foundation. unknown 1(4):16-19.
James S. Findley and Muriel T. Findley. 1989. Circumtropical patterns in butterflyfish communities. unknown 25(1):33-46.
James S. Findley. 1956. Mammals of Clay County South Dakota. unknown 1:1-45.
James S. Findley and Don E. Wilson. 1983. Are bats rare in tropical Africa? unknown 15(4):299-303.
James S. Findley, Thomas H Kunz, J. Gaisler, Karl F. Koopman, P. A. Racey, G. Marimuthu, M. L. Augee, G. R. Horst. 1995. International bat research conferences: Historical glimpses. unknown 36:132-136.
Robert L. Rausch. 1948. Notes on Cestodes of the Genus Andrya Railliet, 1883, with the Description of <i>A. ondatrae</i> n. sp. (Cestoda: Anoplocephalidae). unknown 67(2):187-191.
Georges Dubois and Robert L. Rausch. 1948. Seconde contribution a l'etude des 'Strigeides' (Trematoda) Nord-Americains. unknown 71:29-30.
J. F. Denton and Robert L. Rausch. 1949. The occurrence of <i>Platynosomum illiciens</i> (Braun, 1901) in a North American hawk. unknown 16:7-9.
Robert L. Rausch and E. L. Schiller. 1949. Some observations on cestodes of the genus <i>Paranoplocephala</i> Luehe, parasitic in North American voles (<i>Microtus</i> spp.). unknown 16:23-31.
Harley J. Van Cleave and Robert L. Rausch. 1951. The acanthocephalan parasites of eider ducks. unknown 18:81-84.
Robert L. Rausch. 1951. Studien an der Helminthenfauna von Alaska. IV. <i>Haploparaxis galli</i> n. sp., ein Cestode aus dem Schneehuhn, <i>Laopus rupestris </i>(Gmelin). unknown 15:1-3.
Robert L. Rausch. 1953. Animal-borne diseases in Alaska and their public health significance. unknown 2(1):1165-1170.
Robert L. Rausch. 1956. Studies on the helminth fauna of Alaska. XXVIII.  The description and occurrence of <i>Diphyllobothrium dalliae</i>  n. sp.  (Cestoda). unknown 75(2):180-187.
Robert L. Rausch and J. Yamashita. 1957. The occurrence of <i>Echinococcus multilocularis</i> Leuckart, 1863, in Japan. unknown 24(2):128-133.
Robert L. Rausch. 1958. <i>Echinococcus multilocularis</i> infection. unknown 2:597-610.
Robert L. Rausch. 1959. Studies on the helminth fauna of Alaska. XXXV. On the identity of certain cestodes (Taeniidae) from foxes. unknown 26(2):125-131.
Robert L. Rausch. 1962. Trichinellosis in the Arctic. unknown:80-86.
Robert L. Rausch. 1969. Diphyllobothriid cestodes from the Hawaiian monk seal, <i>Monachus schauinslandi</i> Matschie, from Midway Atoll. unknown 26(4):947-956.
Robert L. Rausch. 1973. Postmortem findings in some marine mammals and birds following the Cannikin Test on Amchitka Island.  U.S. Atomic Energy Commission Report NVO-130. unknown:-.
Robert L. Rausch. 1985. <i>Gruitaenia gruis</i> n. sp. (Cestoda: Dilepididae) from the Sandhill Crane, <i>Grus canadensis</i> (L.) in Alaska. (Studies on the helminth fauna of Alaska. LII). unknown 22:153-159.
Voitto Haukisalmi, Robert L. Rausch, Heikki Henttonen. 2005. Morphological characterization of <i>Paranoplocephala bairdi</i> (Schad, 1954) (Cestoda: Anoplocephlidae) in heather voles <i>Phenacomys</i> spp. and tree voles <i>Arborimus</i> spp., and related species in voles and lemmings (Muridae: Arvicolinae). unknown 52:311-321.
David Smith. 1989. The sawfly genus Arge (Hymenoptera; Argidae) in the Western Hemisphere. unknown 115(2):83-205.
Publio Gonzalez-Dominguez, Yadeeh E. Sawyer, Mario Avila, Anibal Armien, Blas Armien, Joseph A. Cook. 2010. Variation in cytochrome-b haplotypes suggests a new species of <i>Zygodontomys</i> (Rodentia: Cricetidae) endemic to Isla Coiba, Panama. unknown 27(4):660-665.
    - MSB:Mamm @ 5
Joseph A. Cook. 2010. Characterization of the rabbit agouti signaling protein (ASIP) gene: Transcripts and phylogenetic analyses and identification of the causative mutation of the nonagouti black coat colour. unknown 95(3):166-175.
Luca Fontanesi, Lionel Forestier, Daniel Allain, Emilio Scotti, Francesca Beretti, Severine Deretz-Picoulet, Elena Pecchioli, Cristiano Vernesi, Terence J. Robinson, Jason L. Malaney, Vincenzo Russo, Ahmad Oulmouden. 2010. Characterization of the rabbit agouti signaling protein (ASIP) gene: Transcripts and phylogenetic analyses and identification of the causative mutation of the nonagouti black coat color. unknown 95(3):166-175.
Molecular phylogenetics of the elephant schistosome <i>Bivitellobilharzia loxodontae</i> (Trematoda: Schistosomatidae) from the Central African Republic
    - MSB:Para @ 5
    - MSB:Host @ 1
Barnes, A. M.; Tipton, V. J.; and Wildie, J. A. (1977) "The subfamily Anomiopsyllinae (Hystrichopsyllidae: Siphonaptera). I. A revision of the genus Anomiopsyllus Baker," Great Basin Naturalist: Vol. 37: No. 2, Article 2.
mkoo commented 5 years ago

AWG: 3/7/2019: Deprecate Priority-critical. Individuals will tackle and cleanup on their own in time for next month's Issues Meeting. @dustymc Can we please have a working SQL for checking our progress?

dustymc commented 5 years ago 
 select distinct publication_id,full_citation from (
 select publication.publication_id,full_citation from publication where lower(full_citation) like '%unknown%'
union 
select publication.publication_id,full_citation from publication,publication_agent where publication.publication_id=publication_agent.publication_id and agent_id=0
union
select publication.publication_id,full_citation from publication where publication_id not in (select publication_id from publication_agent)
)
ccicero commented 5 years ago

Just some notes for the cleanup: (1) add DOI at the same time, (2) may need to update author in full citation manually (?).

dustymc commented 5 years ago

DOI

That would be amazing. With DOI we can talk to the world, without we can't really successfully talk to ourselves (eg, duplicate publications are still being created).

update author in full citation manually

There are some publications that contain "unknown" in the citation. There is no link between the citation and Agents, so those should be updated.

atrox10 commented 5 years ago

I can try to fix the herp review/copeia obvious herp ones. Note that Herp Review, Southwestern Naturalist and older Zootaxa (and possibly older Herp journals) don't have DOIs associated with articles. So don't get rid of those without DOIs! please

atrox10 commented 5 years ago

I have fixed all the herps, maybe Chris Conroy or someone wants to fix the mammal ones? They all seem to be MVZ pubs!!

dustymc commented 5 years ago

@atrox10 DOI isn't mandatory but it is REALLY useful - I won't delete anything.

Here are some duplicates - they're getting hard to find!

@campmlc 


select full_citation from publication where full_citation not like '%Field Notes%' and regexp_replace(full_citation,'[^A-Za-z]','X') in (
select regexp_replace(full_citation,'[^A-Za-z]','X') from publication having count(*)>1 group by regexp_replace(full_citation,'[^A-Za-z]','X')
) order by full_citation;

Fernando Torres-Perez, R. Eduardo Palma, Brian Hjelle, Marcela Ferres, Joseph A. Cook. 2009. Andes virus infections in t
he rodent reservoir and in humans vary across contrasting landscapes in Chile. Infection, Genetics and Evolution 10:820-
825.

Fernando Torres-Perez, R. Eduardo Palma, Brian Hjelle, Marcela Ferres, Joseph A. Cook. 2010. Andes virus infections in t
he rodent reservoir and in humans vary across contrasting landscapes in Chile. Infection, Genetics and Evolution 10:820-
825.

Terry L. Yates. 1984. The role of voucher specimens in mammal collections: characterization and funding responsibilities
. Acta Zoologica 170(2):81-82.

Terry L. Yates. 1985. The role of voucher specimens in mammal collections: characterization and funding responsibilities
. Acta Zoologica 170(2):81-82.
atrox10 commented 5 years ago

Ok thanks, I finished the herps,, only 1 had a DOI. Chris is working on the mammal unknowns. Can we just delete the dupes?. As long as the don’t have associated citations? Or does someone need to check them?

On Thu, Mar 7, 2019 at 4:03 PM dustymc notifications@github.com wrote:

@atrox10 https://github.com/atrox10 DOI isn't mandatory but it is REALLY useful - I won't delete anything.

Here are some duplicates - they're getting hard to find!

@campmlc https://github.com/campmlc

select full_citation from publication where full_citation not like '%Field Notes%' and regexp_replace(full_citation,'[^A-Za-z]','X') in ( select regexp_replace(full_citation,'[^A-Za-z]','X') from publication having count(*)>1 group by regexp_replace(full_citation,'[^A-Za-z]','X') ) order by full_citation;

Fernando Torres-Perez, R. Eduardo Palma, Brian Hjelle, Marcela Ferres, Joseph A. Cook. 2009. Andes virus infections in t he rodent reservoir and in humans vary across contrasting landscapes in Chile. Infection, Genetics and Evolution 10:820- 825.

Fernando Torres-Perez, R. Eduardo Palma, Brian Hjelle, Marcela Ferres, Joseph A. Cook. 2010. Andes virus infections in t he rodent reservoir and in humans vary across contrasting landscapes in Chile. Infection, Genetics and Evolution 10:820- 825.

Terry L. Yates. 1984. The role of voucher specimens in mammal collections: characterization and funding responsibilities . Acta Zoologica 170(2):81-82.

Terry L. Yates. 1985. The role of voucher specimens in mammal collections: characterization and funding responsibilities . Acta Zoologica 170(2):81-82.

— You are receiving this because you were mentioned.

Reply to this email directly, view it on GitHub https://github.com/ArctosDB/arctos/issues/1570#issuecomment-470750877, or mute the thread https://github.com/notifications/unsubscribe-auth/AESS8dFSyh5s6pkMvR1eAbZbC5uYu17Hks5vUai9gaJpZM4UoSSR .

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dustymc commented 5 years ago

Yes you can delete the dups if they're not used - they're slightly different so it may not be completely arbitrary.

Here's some better SQL

 select 'unknown_title' r,publication.publication_id,full_citation, guid_prefix from publication,citation, cataloged_item,collection
      where publication.publication_id=citation.publication_id (+) and
      citation.collection_object_id=cataloged_item.collection_object_id (+) and
      cataloged_item.collection_id=collection.collection_id (+) and
      lower(full_citation) like '%unknown%' group by publication.publication_id,full_citation, guid_prefix
      union
 select 'agent_zero' r,publication.publication_id,full_citation, guid_prefix from publication,publication_agent,citation, cataloged_item,collection
      where publication.publication_id=citation.publication_id (+) and
      citation.collection_object_id=cataloged_item.collection_object_id (+) and
      cataloged_item.collection_id=collection.collection_id (+) and
      publication.publication_id=publication_agent.publication_id and
      agent_id=0
    group by publication.publication_id,full_citation, guid_prefix
    union
    select 'no_authors' r,publication.publication_id,full_citation, guid_prefix from publication,citation, cataloged_item,collection where 
publication.publication_id=citation.publication_id (+) and
      citation.collection_object_id=cataloged_item.collection_object_id (+) and
      cataloged_item.collection_id=collection.collection_id (+) and
      publication.publication_id   not in (select publication_id from publication_agent)

Summary:

select r, guid_prefix, count(*) from(
 select 'unknown_title' r,publication.publication_id,full_citation, guid_prefix from publication,citation, cataloged_item,collection
      where publication.publication_id=citation.publication_id (+) and
      citation.collection_object_id=cataloged_item.collection_object_id (+) and
      cataloged_item.collection_id=collection.collection_id (+) and
      lower(full_citation) like '%unknown%' group by publication.publication_id,full_citation, guid_prefix
      union
 select 'agent_zero' r,publication.publication_id,full_citation, guid_prefix from publication,publication_agent,citation, cataloged_item,collection
      where publication.publication_id=citation.publication_id (+) and
      citation.collection_object_id=cataloged_item.collection_object_id (+) and
      cataloged_item.collection_id=collection.collection_id (+) and
      publication.publication_id=publication_agent.publication_id and
      agent_id=0
    group by publication.publication_id,full_citation, guid_prefix
    union
    select 'no_authors' r,publication.publication_id,full_citation, guid_prefix from publication,citation, cataloged_item,collection where 
publication.publication_id=citation.publication_id (+) and
      citation.collection_object_id=cataloged_item.collection_object_id (+) and
      cataloged_item.collection_id=collection.collection_id (+) and
      publication.publication_id   not in (select publication_id from publication_agent)
 21   ) group by r,guid_prefix order by r,guid_prefix     ;

R                   GUID_PREFIX                            COUNT(*)
--------------------------------------- ------------------------------------------------------------ ----------
agent_zero              MSB:Host                                  1
agent_zero              MSB:Para                                  1
agent_zero              UAM:EH                                    1
agent_zero                                                   32
no_authors              CHAS:Egg                                  1
no_authors              DMNS:Bird                                 1
no_authors              DMNS:Egg                                  1
no_authors              DMNS:Mamm                                 4
no_authors              KNWR:Ento                                 1
no_authors              KWP:Ento                                  2
no_authors              MLZ:Bird                                 47
no_authors              MSB:Mamm                                 27
no_authors              MSB:Para                                  1
no_authors              MVZ:Mamm                                  6
no_authors              UAM:Bird                                  7
no_authors              UAM:EH                                    3
no_authors              UAM:Ento                                 37
no_authors              UAM:Herb                                  1
no_authors              UAM:Inv                                   1
no_authors              UAM:Mamm                                  8
no_authors              UAMObs:Ento                             383
no_authors              UTEP:Herp                                 1
no_authors              UTEP:Mamm                                 2
no_authors              UWBM:Herp                                 1
no_authors                                                  128
unknown_title               MSB:Mamm                                  1
unknown_title                                                    57

27 rows select

Maybe we should delete the low-data stuff that nobody's using???

campmlc commented 5 years ago

I fixed these two. I'll work on MSB related mammal pubs.

On Thu, Mar 7, 2019 at 5:03 PM dustymc notifications@github.com wrote:

@atrox10 https://github.com/atrox10 DOI isn't mandatory but it is REALLY useful - I won't delete anything.

Here are some duplicates - they're getting hard to find!

@campmlc https://github.com/campmlc

select full_citation from publication where full_citation not like '%Field Notes%' and regexp_replace(full_citation,'[^A-Za-z]','X') in ( select regexp_replace(full_citation,'[^A-Za-z]','X') from publication having count(*)>1 group by regexp_replace(full_citation,'[^A-Za-z]','X') ) order by full_citation;

Fernando Torres-Perez, R. Eduardo Palma, Brian Hjelle, Marcela Ferres, Joseph A. Cook. 2009. Andes virus infections in t he rodent reservoir and in humans vary across contrasting landscapes in Chile. Infection, Genetics and Evolution 10:820- 825.

Fernando Torres-Perez, R. Eduardo Palma, Brian Hjelle, Marcela Ferres, Joseph A. Cook. 2010. Andes virus infections in t he rodent reservoir and in humans vary across contrasting landscapes in Chile. Infection, Genetics and Evolution 10:820- 825.

Terry L. Yates. 1984. The role of voucher specimens in mammal collections: characterization and funding responsibilities . Acta Zoologica 170(2):81-82.

Terry L. Yates. 1985. The role of voucher specimens in mammal collections: characterization and funding responsibilities . Acta Zoologica 170(2):81-82.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ArctosDB/arctos/issues/1570#issuecomment-470750877, or mute the thread https://github.com/notifications/unsubscribe-auth/AOH0hBI_e3sGYuexpMMSCzVXzVHRCF1Hks5vUai9gaJpZM4UoSSR .

atrox10 commented 5 years ago

All MVZ unknown author pubs fixed, so no unknown as author for MVZ now! (yay Carol and Chris!)

dustymc commented 5 years ago

see what I can magic for no-authors

dustymc commented 5 years ago

Elapsed: 00:00:07.28 select 'unknown_title' r,publication.publication_id,full_citation, guid_prefix from publication,citation, cataloged_item,collection where publication.publication_id=citation.publication_id (+) and citation.collection_object_id=cataloged_item.collection_object_id (+) and cataloged_item.collection_id=collection.collection_id (+) and 5 lower(full_citation) like '%unknown%' group by publication.publication_id,full_citation, guid_prefix;

R PUBLICATION_ID

FULL_CITATION

GUID_PREFIX

unknown_title 10005108 Georges Dubois and Robert L. Rausch. 1948. Seconde contribution a l'etude des 'Strigeides' (Trematoda) Nord-Americains. unknown 71:29-30.

unknown_title 10005392 Publio Gonzalez-Dominguez, Yadeeh E. Sawyer, Mario Avila, Anibal Armien, Blas Armien, Joseph A. Cook. 2010. Variation in cytochrome-b haplotypes suggests a new species of Zygodontomys (Rodentia: Cricetidae) endemic to Isla Coiba, Pan ama. unknown 27(4):660-665. MSB:Mamm

unknown_title 10005066 James S. Findley, Thomas H Kunz, J. Gaisler, Karl F. Koopman, P. A. Racey, G. Marimuthu, M. L. Augee, G. R. Horst. 1995. International bat research conferences: Historical glimpses. unknown 36:132-136.

unknown_title 10005106 Robert L. Rausch. 1948. Notes on Cestodes of the Genus Andrya Railliet, 1883, with the Description of A. ondatrae n. sp. (Cestoda: Anoplocephalidae). unknown 67(2):187-191.

unknown_title 10004891 Brian Hjelle and Fernando Torres-Perez. 2010. Hantaviruses in the Americas and Their Role as Emerging Pathogens. unknown 2:2559-2586.

unknown_title 10005188 Robert L. Rausch. 1962. Trichinellosis in the Arctic. unknown:80-86.

unknown_title 10005061 James S. Findley and Don E. Wilson. 1983. Are bats rare in tropical Africa? unknown 15(4):299-303.

unknown_title 10005295 Robert L. Rausch. 1985. Gruitaenia gruis n. sp. (Cestoda: Dilepididae) from the Sandhill Crane, Grus canadensi s (L.) in Alaska. (Studies on the helminth fauna of Alaska. LII). unknown 22:153-159.

unknown_title 10005111 J. F. Denton and Robert L. Rausch. 1949. The occurrence of Platynosomum illiciens (Braun, 1901) in a North Americ an hawk. unknown 16:7-9.

unknown_title 10005245 Robert L. Rausch. 1973. Postmortem findings in some marine mammals and birds following the Cannikin Test on Amchitka Isl and. U.S. Atomic Energy Commission Report NVO-130. unknown:-.

unknown_title 10005026 James S. Findley. 1956. Mammals of Clay County South Dakota. unknown 1:1-45.

unknown_title 10005136 Harley J. Van Cleave and Robert L. Rausch. 1951. The acanthocephalan parasites of eider ducks. unknown 18:81-84.

unknown_title 10005382 David Smith. 1989. The sawfly genus Arge (Hymenoptera; Argidae) in the Western Hemisphere. unknown 115(2):83-205.

unknown_title 10005163 Robert L. Rausch. 1956. Studies on the helminth fauna of Alaska. XXVIII. The description and occurrence of Diphyllob othrium dalliae n. sp. (Cestoda). unknown 75(2):180-187.

unknown_title 10005174 Robert L. Rausch. 1958. Echinococcus multilocularis infection. unknown 2:597-610.

unknown_title 10005112 Robert L. Rausch and E. L. Schiller. 1949. Some observations on cestodes of the genus Paranoplocephala Luehe, par asitic in North American voles (Microtus spp.). unknown 16:23-31.

unknown_title 10004997 James S. Findley and Muriel T. Findley. 1989. Circumtropical patterns in butterflyfish communities. unknown 25(1):33-46.

unknown_title 10005222 Robert L. Rausch. 1969. Diphyllobothriid cestodes from the Hawaiian monk seal, Monachus schauinslandi Matschie, f rom Midway Atoll. unknown 26(4):947-956.

unknown_title 10005433 Joseph A. Cook. 2010. Characterization of the rabbit agouti signaling protein (ASIP) gene: Transcripts and phylogenetic analyses and identification of the causative mutation of the nonagouti black coat colour. unknown 95(3):166-175.

unknown_title 10005178 Robert L. Rausch. 1959. Studies on the helminth fauna of Alaska. XXXV. On the identity of certain cestodes (Taeniidae) f rom foxes. unknown 26(2):125-131.

unknown_title 10005437 Luca Fontanesi, Lionel Forestier, Daniel Allain, Emilio Scotti, Francesca Beretti, Severine Deretz-Picoulet, Elena Pecch ioli, Cristiano Vernesi, Terence J. Robinson, Jason L. Malaney, Vincenzo Russo, Ahmad Oulmouden. 2010. Characterization of the rabbit agouti signaling protein (ASIP) gene: Transcripts and phylogenetic analyses and identification of the caus ative mutation of the nonagouti black coat color. unknown 95(3):166-175.

unknown_title 10004628 Gabor R. Racz and William L. Gannon. 2005. Improving collection maintenance through innovation: bar-code labeling to tra ck specimens in the processing stream. unknown 1:227-241.

unknown_title 10005137 Robert L. Rausch. 1951. Studien an der Helminthenfauna von Alaska. IV. Haploparaxis galli n. sp., ein Cestode aus dem Schneehuhn, Laopus rupestris (Gmelin). unknown 15:1-3.

unknown_title 10005152 Robert L. Rausch. 1953. Animal-borne diseases in Alaska and their public health significance. unknown 2(1):1165-1170.

unknown_title 10004930 Terry L. Yates and James Estes. 1991. Support for Biodiversity research at the National Science Foundation. unknown 1(4) :16-19.

unknown_title 10005169 Robert L. Rausch and J. Yamashita. 1957. The occurrence of Echinococcus multilocularis Leuckart, 1863, in Japan. unknown 24(2):128-133.

unknown_title 10004838 Dr. Carol W. Allison. 1973. Late Proterozoic Tindir Group, Alaska . unknown unknown(unknown):65-68.

unknown_title 10005359 Voitto Haukisalmi, Robert L. Rausch, Heikki Henttonen. 2005. Morphological characterization of Paranoplocephala baird i (Schad, 1954) (Cestoda: Anoplocephlidae) in heather voles Phenacomys spp. and tree voles Arborimus s pp., and related species in voles and lemmings (Muridae: Arvicolinae). unknown 52:311-321.

Jegelewicz commented 5 years ago

UTEP Authors added. Will get a student to work on this next week - I have someone in mind....

DerekSikes commented 5 years ago

I added the journal for this:

unknown_title 10005382 David Smith. 1989. The sawfly genus Arge (Hymenoptera; Argidae) in the Western Hemisphere. unknown 115(2):83-205.

On Thu, Mar 14, 2019 at 11:56 AM Teresa Mayfield-Meyer < notifications@github.com> wrote:

UTEP Authors added. Will get a student to work on this next week - I have someone in mind....

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dustymc commented 5 years ago

suggest two triggers

The forms already "require" one author - that's about the best we can do with that.

dustymc commented 5 years ago

Current data:

R                   GUID_PREFIX                            COUNT(*)
--------------------------------------- ------------------------------------------------------------ ----------
no_authors              DMNS:Bird                                 1
no_authors              DMNS:Egg                                  1
no_authors              DMNS:Mamm                                 1
no_authors              KNWR:Ento                                 1
no_authors              KWP:Ento                                  2
no_authors              MLZ:Bird                                 47
no_authors              MSB:Mamm                                  5
no_authors              MVZ:Mamm                                  6
no_authors              UAM:Bird                                  7
no_authors              UAM:EH                                    3
no_authors              UAM:Ento                                 37
no_authors              UAM:Herb                                  1
no_authors              UAM:Inv                                   1
no_authors              UAM:Mamm                                  8
no_authors              UAMObs:Ento                             173
no_authors              UWBM:Herp                                 1
no_authors                                                  125
unknown_title                                                    24
dustymc commented 5 years ago

trigger created to disallow agent_id=0 in publication_agent

dustymc commented 5 years ago

Publication trigger now contains

Full Citation contains _unknown_. Prefix Full Citation with an asterisk if this is an accurate representation of the data. DO NOT indicate uncertainty in publication titles.
dustymc commented 3 years ago

I now find 447 publications without authors or with 'unknown' in the title - CSV attached.

temp_funky_publications.csv.zip

This was to happen by April 2019 - can we try something other than https://github.com/ArctosDB/arctos/issues/1570#issuecomment-470671827 now?

Summary:


       r       | guid_prefix | count 
---------------+-------------+-------
 no_authors    | DMNS:Mamm   |     1
 no_authors    | MSB:Para    |     1
 no_authors    | KNWR:Ento   |     1
 no_authors    | UAM:Bird    |     7
 no_authors    | KWP:Ento    |     2
 no_authors    | UAM:Mamm    |     7
 no_authors    | UWBM:Herp   |     1
 no_authors    |             |   127
 no_authors    | UAM:Ento    |    38
 no_authors    | UAM:Herb    |     1
 unknown_title |             |    24
 no_authors    | UTEP:Herp   |     4
 no_authors    | MVZ:Mamm    |     7
 no_authors    | UCM:Mamm    |     1
 no_authors    | DMNS:Bird   |     2
 no_authors    | MSB:Mamm    |     6
 no_authors    | UTEP:Herb   |     1
 no_authors    | UAM:EH      |     3
 no_authors    | MLZ:Bird    |    47
 no_authors    | UAMObs:Ento |   165
 no_authors    | UAM:Inv     |     1

Postgres SQL:

select 
  'unknown_title' r,
  publication.publication_id,
  full_citation, 
  guid_prefix 
  from 
  publication
  left outer join citation on publication.publication_id=citation.publication_id 
  left outer join cataloged_item on citation.collection_object_id=cataloged_item.collection_object_id
  left outer join collection on cataloged_item.collection_id=collection.collection_id
      where
      lower(full_citation) like '%unknown%' group by publication.publication_id,full_citation, guid_prefix
      union
 select 'agent_zero' r,
 publication.publication_id,
 full_citation, 
 guid_prefix 
 from 
 publication
 inner join publication_agent on publication.publication_id=publication_agent.publication_id
  left outer join citation on publication.publication_id=citation.publication_id
 left outer join cataloged_item on citation.collection_object_id=cataloged_item.collection_object_id
 left outer join collection on cataloged_item.collection_id=collection.collection_id
      where 
      agent_id=0
    group by publication.publication_id,full_citation, guid_prefix
    union
    select 
    'no_authors' r,
    publication.publication_id,
    full_citation, 
    guid_prefix 
    from publication
  left outer join citation on publication.publication_id=citation.publication_id 
  left outer join cataloged_item on citation.collection_object_id=cataloged_item.collection_object_id
  left outer join collection on cataloged_item.collection_id=collection.collection_id
where 
      publication.publication_id   not in (select publication_id from publication_agent)

;
campmlc commented 3 years ago

I fixed the MSB:Mamm ones. To make this process easier, I suggest making the required "author" role be a yellow field, like all the other required fields in the Edit Publications form. Otherwise, there is a cryptic error message. Do we have a standard process for dealing with pubs that cannot be linked to dois, except for adding a remark?

On Wed, Apr 28, 2021 at 10:07 AM dustymc @.***> wrote:

  • [EXTERNAL]*

I now find 447 publications without authors or with 'unknown' in the title

  • CSV attached.

temp_funky_publications.csv.zip https://github.com/ArctosDB/arctos/files/6393222/temp_funky_publications.csv.zip

This was to happen by April 2019 - can we try something other than #1570 (comment) https://github.com/ArctosDB/arctos/issues/1570#issuecomment-470671827 now?

Summary:

   r       | guid_prefix | count

---------------+-------------+------- no_authors | DMNS:Mamm | 1 no_authors | MSB:Para | 1 no_authors | KNWR:Ento | 1 no_authors | UAM:Bird | 7 no_authors | KWP:Ento | 2 no_authors | UAM:Mamm | 7 no_authors | UWBM:Herp | 1 no_authors | | 127 no_authors | UAM:Ento | 38 no_authors | UAM:Herb | 1 unknown_title | | 24 no_authors | UTEP:Herp | 4 no_authors | MVZ:Mamm | 7 no_authors | UCM:Mamm | 1 no_authors | DMNS:Bird | 2 no_authors | MSB:Mamm | 6 no_authors | UTEP:Herb | 1 no_authors | UAM:EH | 3 no_authors | MLZ:Bird | 47 no_authors | UAMObs:Ento | 165 no_authors | UAM:Inv | 1

Postgres SQL:

select 'unknown_title' r, publication.publication_id, full_citation, guid_prefix from publication left outer join citation on publication.publication_id=citation.publication_id left outer join cataloged_item on citation.collection_object_id=cataloged_item.collection_object_id left outer join collection on cataloged_item.collection_id=collection.collection_id where lower(full_citation) like '%unknown%' group by publication.publication_id,full_citation, guid_prefix union select 'agent_zero' r, publication.publication_id, full_citation, guid_prefix from publication inner join publication_agent on publication.publication_id=publication_agent.publication_id left outer join citation on publication.publication_id=citation.publication_id left outer join cataloged_item on citation.collection_object_id=cataloged_item.collection_object_id left outer join collection on cataloged_item.collection_id=collection.collection_id where agent_id=0 group by publication.publication_id,full_citation, guid_prefix union select 'no_authors' r, publication.publication_id, full_citation, guid_prefix from publication left outer join citation on publication.publication_id=citation.publication_id left outer join cataloged_item on citation.collection_object_id=cataloged_item.collection_object_id left outer join collection on cataloged_item.collection_id=collection.collection_id where publication.publication_id not in (select publication_id from publication_agent)

;

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dustymc commented 3 years ago

fixed

Excellent, here's new data.

temp_funky_publications(1).csv.zip

And the summary


       r       | guid_prefix | count 
---------------+-------------+-------
 no_authors    | KNWR:Ento   |     1
 no_authors    | UAMObs:Ento |   165
 no_authors    | UAM:Herb    |     1
 no_authors    | UAM:EH      |     3
 unknown_title |             |    24
 no_authors    | UCM:Mamm    |     1
 no_authors    | MLZ:Bird    |    47
 no_authors    | UAM:Ento    |    38
 no_authors    | UWBM:Herp   |     1
 no_authors    | MVZ:Mamm    |     3
 no_authors    | MSB:Para    |     1
 no_authors    |             |   127
 no_authors    | UTEP:Herb   |     1
 no_authors    | UAM:Mamm    |     7
 no_authors    | DMNS:Mamm   |     1
 no_authors    | UAM:Bird    |     7
 no_authors    | UAM:Inv     |     1
 no_authors    | UTEP:Herp   |     4
 no_authors    | KWP:Ento    |     2
 no_authors    | DMNS:Bird   |     2

standard process f

I don't think so, other than https://handbook.arctosdb.org/documentation/publications.html#doi

yellow

I'll update.

campmlc commented 3 years ago

MSB Para fixed.

On Wed, Apr 28, 2021 at 10:40 AM dustymc @.***> wrote:

  • [EXTERNAL]*

fixed

Excellent, here's new data.

temp_funky_publications(1).csv.zip https://github.com/ArctosDB/arctos/files/6393407/temp_funky_publications.1.csv.zip

And the summary

   r       | guid_prefix | count

---------------+-------------+------- no_authors | KNWR:Ento | 1 no_authors | UAMObs:Ento | 165 no_authors | UAM:Herb | 1 no_authors | UAM:EH | 3 unknown_title | | 24 no_authors | UCM:Mamm | 1 no_authors | MLZ:Bird | 47 no_authors | UAM:Ento | 38 no_authors | UWBM:Herp | 1 no_authors | MVZ:Mamm | 3 no_authors | MSB:Para | 1 no_authors | | 127 no_authors | UTEP:Herb | 1 no_authors | UAM:Mamm | 7 no_authors | DMNS:Mamm | 1 no_authors | UAM:Bird | 7 no_authors | UAM:Inv | 1 no_authors | UTEP:Herp | 4 no_authors | KWP:Ento | 2 no_authors | DMNS:Bird | 2

standard process f

I don't think so, other than https://handbook.arctosdb.org/documentation/publications.html#doi

yellow

I'll update.

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cjconroy commented 3 years ago

MVZ mammals fixed, but found a duplicate. Both of these, Miguel Camacho Sanchez. 2017. Evolution in Sundaland: . One had an author, but no citations, the other citation but no author. both have authors and cited specimens now. What's the best way to delete one of them?

dustymc commented 3 years ago

If there are few citations you can just manually delete from one and add to the other. If there are many let me know and I'll figure it out. Once there are no dependencies you should be able to delete the publication.

cjconroy commented 3 years ago

There was only one each. I'll delete a citation and try to delete the pub and see how that goes.

Jegelewicz commented 3 years ago

Fixed UTEP and MSB Para - all the rest are NOT associated with a GUID Prefix that I can see.

Jegelewicz commented 3 years ago

Is there anything else we need to do here? What I find today are about 390 no-author pubs and 24 with some form of "unknown" in the title.

Jegelewicz commented 3 years ago

Fixed some of the unknown titles.

dustymc commented 3 years ago

The "unknown" look like mostly MSB and easy (??) fixes.

I'm not sure what to do with the no-authors - call it good and close? They'll probably eventually get authors since the UI is requiring that to save.

select 'unknown_title' r, publication.publication_id, full_citation,       guid_prefix 
from 
publication
left outer join citation on publication.publication_id=citation.publication_id
left outer join cataloged_item on citation.collection_object_id=cataloged_item.collection_object_id
left outer join collection on cataloged_item.collection_id=collection.collection_id
where  
lower(publication.full_citation) like '%unknown%' 
group by publication.publication_id,full_citation, guid_prefix
       r       | publication_id |                                                                                                                                                                                                                  full_citation                                                                                                                                                                                                                   | guid_prefix 
---------------+----------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------
 unknown_title |       10005026 | James S. Findley. 1956. Mammals of Clay County South Dakota. unknown 1:1-45.                                                                                                                                                                                                                                                                                                                                                                     | 
 unknown_title |       10005066 | James S. Findley, Thomas H Kunz, J. Gaisler, Karl F. Koopman, P. A. Racey, G. Marimuthu, M. L. Augee, G. R. Horst. 1995. International bat research conferences: Historical glimpses. unknown 36:132-136.                                                                                                                                                                                                                                        | 
 unknown_title |       10005108 | Georges Dubois and Robert L. Rausch. 1948. Seconde contribution a l'etude des 'Strigeides' (Trematoda) Nord-Americains. unknown 71:29-30.                                                                                                                                                                                                                                                                                                        | 
 unknown_title |       10005136 | Harley J. Van Cleave and Robert L. Rausch. 1951. The acanthocephalan parasites of eider ducks. unknown 18:81-84.                                                                                                                                                                                                                                                                                                                                 | 
 unknown_title |       10005137 | Robert L. Rausch. 1951. Studien an der Helminthenfauna von Alaska. IV. <i>Haploparaxis galli</i> n. sp., ein Cestode aus dem Schneehuhn, <i>Laopus rupestris </i>(Gmelin). unknown 15:1-3.                                                                                                                                                                                                                                                       | 
 unknown_title |       10005152 | Robert L. Rausch. 1953. Animal-borne diseases in Alaska and their public health significance. unknown 2(1):1165-1170.                                                                                                                                                                                                                                                                                                                            | 
 unknown_title |       10005163 | Robert L. Rausch. 1956. Studies on the helminth fauna of Alaska. XXVIII.  The description and occurrence of <i>Diphyllobothrium dalliae</i>  n. sp.  (Cestoda). unknown 75(2):180-187.                                                                                                                                                                                                                                                           | 
 unknown_title |       10005169 | Robert L. Rausch and J. Yamashita. 1957. The occurrence of <i>Echinococcus multilocularis</i> Leuckart, 1863, in Japan. unknown 24(2):128-133.                                                                                                                                                                                                                                                                                                   | 
 unknown_title |       10005174 | Robert L. Rausch. 1958. <i>Echinococcus multilocularis</i> infection. unknown 2:597-610.                                                                                                                                                                                                                                                                                                                                                         | 
 unknown_title |       10005178 | Robert L. Rausch. 1959. Studies on the helminth fauna of Alaska. XXXV. On the identity of certain cestodes (Taeniidae) from foxes. unknown 26(2):125-131.                                                                                                                                                                                                                                                                                        | 
 unknown_title |       10005188 | Robert L. Rausch. 1962. Trichinellosis in the Arctic. unknown:80-86.                                                                                                                                                                                                                                                                                                                                                                             | 
 unknown_title |       10005222 | Robert L. Rausch. 1969. Diphyllobothriid cestodes from the Hawaiian monk seal, <i>Monachus schauinslandi</i> Matschie, from Midway Atoll. unknown 26(4):947-956.                                                                                                                                                                                                                                                                                 | 
 unknown_title |       10005245 | Robert L. Rausch. 1973. Postmortem findings in some marine mammals and birds following the Cannikin Test on Amchitka Island.  U.S. Atomic Energy Commission Report NVO-130. unknown:-.                                                                                                                                                                                                                                                           | 
 unknown_title |       10005295 | Robert L. Rausch. 1985. <i>Gruitaenia gruis</i> n. sp. (Cestoda: Dilepididae) from the Sandhill Crane, <i>Grus canadensis</i> (L.) in Alaska. (Studies on the helminth fauna of Alaska. LII). unknown 22:153-159.                                                                                                                                                                                                                                | 
 unknown_title |       10005437 | Luca Fontanesi, Lionel Forestier, Daniel Allain, Emilio Scotti, Francesca Beretti, Severine Deretz-Picoulet, Elena Pecchioli, Cristiano Vernesi, Terence J. Robinson, Jason L. Malaney, Vincenzo Russo, Ahmad Oulmouden. 2010. Characterization of the rabbit agouti signaling protein (ASIP) gene: Transcripts and phylogenetic analyses and identification of the causative mutation of the nonagouti black coat color. unknown 95(3):166-175. |
Jegelewicz commented 3 years ago

The "unknown" look like mostly MSB and easy (??) fixes.

I've been working on those, but it was wearing me out. Some of the older ones I cannot find. Once I get down to things I can't resolve with Google I'll post here.

I'm not sure what to do with the no-authors - call it good and close?

I was thinking of trying to get a list of the authors from the full citation and adding them in bulk, but many of them include multiple authors and almost all of them format the author names as "Last, F.M." which is drag when the multiple authors are also separated by commas. Given that - I think I agree with you....

Jegelewicz commented 3 years ago

Love how we make Google....

image

image

Jegelewicz commented 3 years ago

Here is what's left:

R PUBLICATION_ID FULL_CITATION GUID_PREFIX
unknown_title 10005066 James S. Findley, Thomas H Kunz, J. Gaisler, Karl F. Koopman, P. A. Racey, G. Marimuthu, M. L. Augee, G. R. Horst. 1995. International bat research conferences: Historical glimpses. unknown 36:132-136.
unknown_title 10005108 Georges Dubois and Robert L. Rausch. 1948. Seconde contribution a l'etude des 'Strigeides' (Trematoda) Nord-Americains. unknown 71:29-30.
unknown_title 10005174 Robert L. Rausch. 1958. Echinococcus multilocularis infection. unknown 2:597-610.
unknown_title 10005188 Robert L. Rausch. 1962. Trichinellosis in the Arctic. unknown:80-86.
unknown_title 10005295 Robert L. Rausch. 1985. Gruitaenia gruis n. sp. (Cestoda: Dilepididae) from the Sandhill Crane, Grus canadensis (L.) in Alaska. (Studies on the helminth fauna of Alaska. LII). unknown 22:153-159.
Jegelewicz commented 3 years ago

OK to close?