An attempt to keep track of how science could be improved
License: Other
This repository is meant to help catalogue issues that have been identified in the research ecosystem, as well as potential or actual measures to address them. Feel free to use it to post your observations and ideas on how the research ecosystem could be improved.
I am thinking of ways to turn this into something more actionable than just another bug list. Here too, your suggestions are welcome.
As per
https://opencitations.net/index/coci/api/v1/references/10.1080/08927014.2015.1137896
I do not have full-text access to the article at 10.1080/08927014.2015.1137896 right now, so cannot verify whether that citation is correct but I doubt it, since that DOI 10.1002/(issn)1521-186x simply points to the homepage of the journal with the ISSN 1521-186x.
Lots of examples of industry X funding research at institution Y.
Here is one for X = fossil fuel industry and Y = Harvard University: Beyond the Endowment
Seen at 0009-0009-0534-1166 (not linking there on purpose):
Archived at
As per
https://doi.org/10.1111/j.1365-2664.2009.01641.x :
This seems to be an image not just in the HTML version but also in the PDF, and even the suggested citation just has empty parentheses for the Chinese textÖ
TY - JOUR
AU - He, Fangliang
TI - Price of prosperity: economic development and biological conservation in China ()
JO - Journal of Applied Ecology
VL - 46
IS - 3
SN - 0021-8901
UR - https://doi.org/10.1111/j.1365-2664.2009.01641.x
DO - https://doi.org/10.1111/j.1365-2664.2009.01641.x
SP - 511
EP - 515
KW - Baiji
KW - Beshanzu fir
KW - biodiversity conservation
KW - China
KW - economic growth
KW - environmental protection
KW - species extinction
KW - invasive species
KW - nature reserves
PY - 2009
AB - Summary 1 In the past three decades China has experienced fundamental changes to its economy, which have transformed it from one of the poorest countries in the world to the third largest economic body. This gain in wealth has, however, been achieved at severe cost to the environment. 2 I review the current state of environmental protection and examine the effectiveness of the existing nature reserves for biological conservation in China. 3 Synthesis and applications. Proactive approaches to environmental management ? including significant investment in science and technology, science-informed land-use policy making and international collaboration ? are necessary for China to significantly slow down or reverse its current environmental problems.
ER -
examples of transcription errors in Mammal Species of the World -
https://github.com/jhpoelen/msw-plazi/blob/main/annotations.csv
In this version, the Wikidata item Repeated Iron-Soot Exposure and Nose-to-brain Transport of Inhaled Ultrafine Particles. (Q47638090) corresponding to the paper Repeated Iron–Soot Exposure and Nose-to-brain Transport of Inhaled Ultrafine Particles has an author (P50) statement pointing to Q90909359 (which back then was labeled "Kent E Pinkerton") with a "series ordinal (P1545)" of 8 and had an ORCID (P496) statement that pointed to https://orcid.org/0000-0001-6868-7572, which is largely empty but features the name "Emilia Laing" and no Kent Pinkerton.
Still in that same version of Repeated Iron-Soot Exposure and Nose-to-brain Transport of Inhaled Ultrafine Particles. (Q47638090), there is an author name string (P2093) statement "Emilia A Laing" with series ordinal 2.
The statements on Q47638090 point to the Europe PMC API call https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28914166%20AND%20SRC:MED&resulttype=core&format=json, which has the above ORCID (of Emilia Laing) associated with Kent Pinkerton (in position 8) and no ORCID for the second author (Emilia Laing)
A similar situation was in Q89716066, whose Europe PMC entry also attaches Emilia Laing's ORCID to Kent Pinkerton's author position: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31645209%20AND%20SRC:MED&resulttype=core&format=json and no ORCID to Emilia Laing's position.
The following Wikidata query lists DOIs in Wikidata that do not start with the obligatory "10":
SELECT ?q ?doi {
?q wdt:P356 ?doi .
FILTER(!REGEX(?doi, "^(10)")).
}
limit 200The first 200 results were
Q47318649 234
Q47318639 235
Q33352073 004
Q47969590 210
Q47713364 217
Q40151820 219
Q48217608 220
Q40151814 230
Q39736360 2324
Q47673028 2397
Q39475445 2401
Q47347051 2505
Q39297625 2600
Q48166698 123
Q47847055 205
Q47969601 208
Q47713398 212
Q47713387 215
Q39836609 2289
Q40789646 2290
Q39836596 2300
Q47840049 232
Q40735977 2321
Q47788024 2333
Q39647519 2350
Q47719557 2378
Q50143665 2423
Q39349039 2426
Q47677059 2430
Q48001880 2491
Q48260062 250
Q38838466 2572
Q38793171 2597
Q47327050 2630
Q47294086 2653
Q47325832 2654
Q38619587 2657
Q50064947 2715
Q47606227 2745
Q49557744 2775
Q50263045 284
Q41926146 288
Q40789640 2296
Q39647531 2342
Q38880141 2348
Q40677212 2361
Q47719568 2377
Q47825322 240
Q47825295 244
Q39240349 2577
Q47565612 2579
Q40291119 259
Q38793180 2594
Q36368505 2595
Q38793167 2598
Q38733609 2616
Q47270823 2675
Q47622511 268
Q41919930 2703
Q47247189 2708
Q50090688 2714
Q47602869 2726
Q46278298 2727
Q47219026 2744
Q39997330 009
Q48217598 227
Q39836627 2284
Q39836621 2286
Q36029533 2330
Q36063633 2340
Q40677254 2344
Q38880146 2355
Q33468286 2359
Q40291125 236
Q47402855 2381
Q39508767 2383
Q38931477 2403
Q39349032 2427
Q39349002 2440
Q39044306 2494
Q47347064 2499
Q47829147 2514
Q38908648 2517
Q36307855 2518
Q38908645 2520
Q40065326 2524
Q38908641 2525
Q38838469 2570
Q40064891 258
Q40217819 2606
Q40178549 2610
Q47327029 2633
Q47327018 2634
Q47294106 2651
Q40039031 2682
Q50114750 2687
Q47669982 2702
Q47849145 2709
Q47748276 2719
Q47748249 2723
Q50064994 2735
Q47219015 2747
Q50045734 2760
Q47622486 277
Q47696746 2770
Q40151828 216
Q48591145 222
Q40706309 2293
Q40789634 2305
Q40789628 2306
Q47820378 2307
Q47739888 2311
Q40659840 2334
Q40677228 2353
Q39293740 2354
Q39647511 2356
Q39508784 2372
Q39508775 2374
Q40582857 2385
Q39475460 2396
Q40615945 2400
Q48020677 2412
Q39349023 2429
Q39349011 2432
Q38965009 2434
Q48260069 249
Q47594782 2493
Q39044301 2500
Q40294651 2527
Q47395087 2571
Q47307523 2574
Q33168624 2599
Q48636149 2611
Q38733613 2614
Q41929635 2625
Q44432359 2629
Q38619590 2650
Q40089569 2664
Q47247212 2696
Q48576647 2700
Q47423734 2716
Q50064990 2734
Q50045745 2758
Q47226427 2765
Q49557713 2779
Q40050473 224
Q40706302 2294
Q40706296 2295
Q40368107 2303
Q47788069 2315
Q38844285 2335
Q40632928 2345
Q36063636 2349
Q48027403 2369
Q39508778 2373
Q47719545 2380
Q36107668 2406
Q40064900 241
Q38931482 2415
Q39349017 2431
Q40087310 2439
Q39348995 2442
Q47594770 2495
Q47594760 2498
Q33440231 251
Q47246389 261
Q41926160 264
Q38687886 2642
Q40130538 2643
Q40089575 2661
Q47990108 2673
Q50114771 2684
Q50090668 2707
Q50090683 2712
Q50064960 2729
Q50064982 2733
Q50045786 2742
Q47408324 2746
Q47606213 2748
Q50045756 2756
Q50045740 2759
Q47204535 2764
Q46252224 2766
Q49557824 2767
Q47204520 2768
Q47204511 2769
Q49557763 2773
Q49557690 2781
Q47756241 281
Q39736366 2322
Q39647525 2343
Q40582874 2375
Q47326971 2637
Q40143073 2638
Q47644877 2669
Q47990118 2672
Q40039037 2681
Q50090639 2692
Q47237543 2717
Q42517208 2737
Each of the following files lists a licence URL with the frequency of it in the CrossRef April 2022 dump. In order of importance:
Unfortunately I do not have the affected DOIs but I can provide them given ~12 hours to process the dump again
Just a quick note for now. Will try to document in more detail later.
The article "Invasive Plant Species in Ghana: Route of Spread, Socio-Economic and Environmental Impact" (DOI: 10.9734/ajee/2023/v20i4445) contains the following sentence in the abstract:
"Findings indicate that the common invasive plants in Ghana are Chromolaema odorata, Calopogonium mucunoides, Cedrella ordorata, Leucaena leucocephala, Broussonetia papyrifera and Prosopis glasdulosa, Azardiracta indica, Echinochloa colona, and Leucaena leucocephala."
Let's look at this more closely:
The taxon names are correct in Table 1 inside the manuscript, albeit with some twists:
The taxon spellings show some further variation throughout the manuscript, e.g. in the image captions.
Seen via https://www.wikidata.org/w/index.php?title=Q114741220&direction=next&oldid=1753769345 .
The data at https://api.crossref.org/v1/works/https://doi.org/10.1002/mmnd.193519340306 indicates the online publication date
but nowhere does it indicate that this was originally published in 1935, even though that year's number was baked into the DOI itself.
"In this study, the European Data portal explores the barriers encountered by data publishers and re-users of Open Data.":
https://www.europeandataportal.eu/en/highlights/barriers-working-open-data
Mônica C. de Britto-Pereira is the second author of Frugivory and Seed Dispersal by Hyla truncata, a Neotropical Treefrog but Crossref has the name (with and without the circonflex) listed in positions 2 and 4:
https://scholia.toolforge.org/work/Q95638519#list-of-authors
https://www.wikidata.org/w/index.php?title=Q95638519&oldid=1902494676
Here are two papers on quite different subjects associated to the same Wikidata entity:
Apart from the DOI, the item's page https://www.wikidata.org/wiki/Q90241568 does not have much information:
The ORCID profile at https://orcid.org/0000-0001-7251-9643 does not have useful information:
But both papers provide (different) information along with this same ORCID.
The first one: https://doi.org/10.1080/22221751.2020.1737579
The second one: https://doi.org/10.1371/journal.pone.0177692
While it is possible that this is indeed the same person (e.g. a biostatistician), my guess is that two people with the same name have been mixed up here, perhaps even by their co-authors upon submission.
Seen via https://author-disambiguator.toolforge.org/names_oauth.php?doit=Look+for+author&name=Xuehong%20Wang :
From “Excellence R Us”: university research and the fetishisation of excellence:
“excellence” is not just unhelpful to realising the goals of research and research communities but actively pernicious
The article goes into quite some detail which could give rise to a good number of more specific tickets here.
The homepage of
https://eoscfuture.eu/
asks for cookie permissions and links to
https://eoscfuture.eu/files/legal/DataProtectionNotice-Citizenship-EN.pdf ,
which currently gives a 404.
As I do not know where their bug tracker is, I am just opening a ticket here.
I also made a quick screencast:
https://youtu.be/rGWOufZB9TI
as per Table 1 in https://doi.org/10.1111/2041-210X.12758 .
Example: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5197301/
Many elements of scholarly infrastructure — e.g. databases, services or tools — are funded through projects, which imperils them on a regular basis.
Some DOIs used to be valid and work fine, yet at some point later in time, they become defunct.
This can be deliberate or not and is often associated with managerial changes, e.g. due to an acquisition of the publisher or a journal switching to a new publisher or being discontinued. This kind of changes can affect DOIs in various ways, e.g. via inactivation of DOI prefixes.
So far, I have not kept track of such cases systematically, but by now, I have seen too many of them to not take note, and this ticket is to help with that.
The first example is 10.1658/1100-9233(2006)17[447:weodas]2.0.co;2, which yields proper metadata via https://api.crossref.org/v1/works/https://doi.org/10.1658/1100-9233(2006)17[447%3AWEODAS]2.0.CO%3B2 but fails to resolve via https://doi.org/10.1658/1100-9233(2006)17[447:weodas]2.0.co;2 , and even a search on the Wiley website does not turn up the target article: https://onlinelibrary.wiley.com/action/doSearch?field1=Title&text1=Wildfire+effects+on+%CE%B2-diversity+and+species+turnover+in+a+forested+landscape&field2=AllField&text2=&field3=AllField&text3=&Ppub= .
It is, however, available via JSTOR under https://www.jstor.org/stable/4096654 .
perverse incentives and hypercompetition are altering academic behavior of re- searchers and universities, reducing scientific progress and increasing unethical actions
The paper provides material for a good number of tickets here, as well as
a conceptual model that describes how emphasis on quantity versus quality can adversely affect true scientific progress
and
ramifications of this environment on the next generation of Science, Technology, Engineering and Mathematics (STEM) re- searchers, public perception, and the future of science itself
and
recommendations that could help our scientific institutions increase productivity and maintain public trust
Seen via https://www.wikidata.org/wiki/Q114742229 :
The DOI 10.1002/MMND.4810520204 would be expected to have its home at https://doi.org/10.1002/MMND.4810520204 and to redirect from there to the resource it is associated with. However, that URL currently redirects to https://www.crossref.org/_deleted-doi/ , which greets the user as follows:
Meanwhile, the metadata at https://api.crossref.org/v1/works/https://doi.org/10.1002/mmnd.4810520204 does not indicate anything about the deprecation:
{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2022,4,2]],"date-time":"2022-04-02T05:01:31Z","timestamp":1648875691644},"reference-count":15,"publisher":"Test accounts","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Mitt. Mus. Nat.kd. Berl., Dtsch entomol."],"published-print":{"date-parts":[[2005]]},"DOI":"10.1002\/mmnd.4810520204","type":"journal-article","created":{"date-parts":[[2007,7,10]],"date-time":"2007-07-10T13:32:41Z","timestamp":1184074361000},"page":"191-216","source":"Crossref","is-referenced-by-count":0,"title":["Description of new genera and species of the subtribe Eunemadina from Chile. New data on other genera (Coleoptera, Leiodidae, Cholevinae)"],"prefix":"10.5555","volume":"52","author":[{"given":"Jos\u00e9 Mar\u00eda Salgado","family":"Costas","sequence":"first","affiliation":[]}],"member":"7822","reference":[{"key":"10.1002\/mmnd.4810520204-BIB1","first-page":"369","volume":"40","author":"Gnaspini","year":"1999","journal-title":"Pap\u00e9is Avulsos de Zoologia"},{"key":"10.1002\/mmnd.4810520204-BIB2","first-page":"1","volume":"1","author":"Jeannel","year":"1936","journal-title":"M\u00e9moires du Mus\u00e9um national d'Histoire naturelle (n.s.)"},{"key":"10.1002\/mmnd.4810520204-BIB3","first-page":"41","volume":"5","author":"Jeannel","year":"1957","journal-title":"Revista Chilena de Entomolog\u00eda"},{"key":"10.1002\/mmnd.4810520204-BIB4","author":"Jeannel","year":"1962","unstructured":"1962. Les Silphidae, Liodidae, Camiaridae et Catopidae de la Paleantarctide occidentale, pp. 481\u2013525. In Delamere, Cl. & (Eds). Biologie de l'Am\u00e9rique Australe 1."},{"key":"10.1002\/mmnd.4810520204-BIB5","author":"Newton","year":"1998","unstructured":"1998. Phylogenetic problems, current classification and generic catalogue of world Leiodidae (including Cholevinae), pp. 41\u2013178. In & (Eds). Phylogeny and evolution of subterranean and endogean Cholevidae (= Leiodidae Cholevinae), proceedings of XX international congress of Entomology. Firenze, 1996. Atti del Museo Regionale di Scienze naturali, Torino."},{"key":"10.1002\/mmnd.4810520204-BIB6","first-page":"37","volume":"9","author":"Peck","year":"1998","journal-title":"Giornale italiano di Entomologia"},{"key":"10.1002\/mmnd.4810520204-BIB7","first-page":"579","volume":"39","author":"Perreau","year":"1989","journal-title":"Archives des Sciences"},{"key":"10.1002\/mmnd.4810520204-BIB8","first-page":"1","volume":"4","author":"Perreau","year":"2000","journal-title":"M\u00e9moires de la Soci\u00e9t\u00e9 Entomologique de France"},{"key":"10.1002\/mmnd.4810520204-BIB9","first-page":"169","volume":"5","author":"Salgado","year":"1991","journal-title":"Elytron"},{"key":"10.1002\/mmnd.4810520204-BIB10","first-page":"159","volume":"14","author":"Salgado","year":"2000","journal-title":"Elytron"},{"key":"10.1002\/mmnd.4810520204-BIB11","doi-asserted-by":"crossref","first-page":"505","DOI":"10.14411\/eje.2002.067","volume":"99","author":"Salgado","year":"2002","journal-title":"European Journal of Entomology"},{"key":"10.1002\/mmnd.4810520204-BIB12","first-page":"245","volume":"57","author":"Szymczakowski","year":"1965","journal-title":"Annales Historico-naturales Musei nationalis Hungarici (Pars Zoologica)"},{"key":"10.1002\/mmnd.4810520204-BIB13","first-page":"397","volume":"16","author":"Szymczakowski","year":"1971","journal-title":"Acta Zoologica Cracoviensia"},{"key":"10.1002\/mmnd.4810520204-BIB14","first-page":"93","volume":"18","author":"Szymczakowski","year":"1973","journal-title":"Acta Zoologica Cracoviensia"},{"key":"10.1002\/mmnd.4810520204-BIB15","first-page":"423","volume":"46","author":"Szymczakowski","year":"1976","journal-title":"Polskie Pismo Entomologiczne"}],"container-title":["Deutsche Entomologische Zeitschrift (neue Folge)"],"original-title":[],"language":"de","deposited":{"date-parts":[[2017,6,17]],"date-time":"2017-06-17T20:41:20Z","timestamp":1497732080000},"score":1,"resource":{"primary":{"URL":"http:\/\/www.crossref.org\/deleted_DOI.html"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005]]},"references-count":15,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2005]]}},"URL":"http:\/\/dx.doi.org\/10.1002\/mmnd.4810520204","relation":{},"ISSN":["1435-1951","1860-1324"],"issn-type":[{"value":"1435-1951","type":"print"},{"value":"1860-1324","type":"electronic"}],"subject":["Insect Science"],"published":{"date-parts":[[2005]]}}}
From https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0294901 :
"The LSID for this publication is: urn:lsid:zoobank.org:pub: XXXXXXX."
Same issue in the PDF and XML versions:
"Sexual Reproduction in Leptosphaeria Avenaria f. sp. Triticea Induced by Wave Lengths of Light Greater than 560 Mμ"
https://api.crossref.org/v1/works/10.1080/00275514.1971.12019190
In the abstract, the unit is used wrongly again:
wavelengths greater than 560 mμ
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