Category Archives: google scholar

27Mar / 2018

Display without Delay: Search, Browse & Cite PLOS Articles with Quick Abstracts from Google Scholar

0000-0002-8715-2896 Working off your mobile device? No problem. We just made it easier to use your phone to find and scan PLOS articles. If you’re someone who’s out in the field more than in the

Posted by in citations, developing world, discovery, featured, google scholar, In the News, innovation, protocols, Publishing, researchers, scientific research, Technology

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06Feb / 2016

A very strange & annoying Google Scholar / Biomed Central "glitch" #GamingMetrics

So I discovered a few days ago I had dozens of new publications in 2015.  Cool right?  Here is a screengrab:



And here is another


Until I realized, well, those were published years ago.  WTF are they doing being listed as 2015?  Clearly some glitch. And then I saw a few Tweets that pointed me to figuring out what was going on.

.





So I responded


And some discussion followed





Fascinating. But I knew my papers were not published as preprints. And that they were published years before Google Scholar was not listing them as being published.

So - what happened? I think I now. These papers were all published in one journal - Standards in Genomic Sciences. The journal used to be published semi-independently by the Genomics Standards Consortium. Then they were transferred to / bout.
ht by / merged with Biomed Central and even the web address was forwarded to BMC where they host the archive of articles from before the transfer.  Then there is a new site with articles from after the transfer.

So when I click on the articles from the Google Scholar site I get to a strange thing.  The articles published before the transfer are also listed on the new site http://standardsingenomics.biomedcentral.com/.

For example - the Complete genome sequence of Sulfurospirillum deleyianum type strain (5175T) is shown here with a 2015 publication date:



Although note the Copyright 2010 little bit.  Which is interesting since this paper was in fact published in 2010.  And you can find it on the other site http://standardsingenomics.org with a 2010 publication data here.



And also in Pubmed and Pubmed Central.





So - even though Biomed Central says the new papers will be in the new site and the old papers will be ket in a separate site that is not what is happening.



For some reasons some of the older papers are now being listed in the new site with a new publication date.  And I assume because Google Scholar scrapes from the journal sites, it found the "new" papers and has now added them to it's clustering collection and has fed them into my publication list.  And despite trying I am not sure how to fix this.

I tried to "unmerge" the new publications to see if somehow the old publications showed up.  But they did not.  So .. am not sure what to do here other than to send this to BMC and Google Scholar, which I will do.  Ahh - the perils of automated systems ...

I note -  this does seem to have possibly temporarily increased my total number of citations since it seems like some of these papers are now being considered twice by Google Scholar but not sure about that.  More digging.





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This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter.
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Posted by in biomed central, fail, google scholar, Publishing

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13Jun / 2013

Weird things coming up from automated Google Scholar searches pointing to hea1thandfitness.com

I noticed some really weird stuff coming up in automated Google Scholar searches.  Example - see this one below:


Scholar Alert: [ metagenomics phylogeny ]

[HTML] Asthma and the Diversity of Fungal Spores in Air

A Pringle - PLoS Pathogens, 2013
... cause and effect between spores and asthma may remain a challenge, metagenomictechnologies
will ... Metagenomics data are likely to provide a very different understanding of the potential diversity ...
(2006) Reconstructing the early evolution of fungi using a six-gene phylogeny. ...

[HTML] Insights inside often the progression amongst Archaea additionally eukaryotic required protein modifier metabolism exposed simply because amongst often the …

T Nunoura, Y Takaki, J Kakuta, S Nishi, J Sugahara… - Life Sciences
... ' ', gives become proposed centred on SSU rRNA gene phylogeny (10 ), unfortunately a ...type II
SSU rRNA gene set identified on the metagenomic library; AB566230. ... Archaea: sides ranging
from microbial ecology and regarding consequence metagenomics GarrettRA KlenkH-P ...


The second paper listed there takes one to a very strange site. It appears to be a pseudo-mirror of the journal site all embedded within the domain "Hea1thandFitness.Com".  Note - this domain name has the number "1" replacing the letter "l" in the domain name - I assume as a trick of sorts.  Clicking on the link takes you to a site for which I have done a screen shot below




The whole thing is weird - with the number instead of the letter and the weird formatting of the site.  Just a tiny glitch?  Well, I don't think so since in some of my other Google Scholar alerts other links to this same domain came up.  See examples below:


Scholar Alert: New articles in Phil Hugenholtz's profile

[HTML] Contrasting Life Strategies involving Viruses that's Infect Photo-certainly to positively not mention Heterotrophic Bacteria, considering that's Revealed by simply Viral …

L Deng, A Gregory, S Yilmaz, BT Poulos, P Hugenholtz…
Ocean infections are usually all-pervasive and also numerous and also play the game main
jobs relating to be the inside overseas biogeochemical menstrual cycles thru their mortality,
horizontally gene transfer, and also mind games about put in relationship metabolism. ...

and

Scholar Alert: [ PhylogenoMics ]

[HTML] PIECE: a collection to help your entire family take also gene rules comparing and then progression

Y Wang, FM You, GR Lazo, MC Luo, R Thilmony… - Life Sciences
... structural repair for retrogenes appearing in the organization for the Populus genome 2009 151
1943 1951 AbstractFREE Full Text Garcia-Espana Mares SunTT Desalle Intron evolution: checking
hypotheses for intron development by consuming phylogenomics for tetraspanins ...

[HTML] Integration of sequence-similarity and therefore practical union information definitely likely surmounted inbuilt factors found in orthology mapping through bacterial …

G Li, Q Ma, X Mao, Y Yin, X Zhu, Y Xu - Life Sciences
... Chen MackeyAJ VermuntJK RoosDS Assessing entire performance of orthology discovery
strategies put to practice found on eukaryotic genomes 2007 e383 CrossRef Medline ZmasekCM
EddySR RIO: analyzing proteomes by automated phylogenomics wearing resampled ...


and

Scholar Alert: [ microbial forensics ]

Effect of modified montmorillonites on the biodegradation and adsorption of biomarkers such as hopanes, steranes and diasteranes

UC Ugochukwu, IM Head, DAC Manning - 2013
... Several studies have demonstrated that some solid sur- faces such as clay minerals are able
to stimulate microbial ... Indigenous microbial cells of Whitley Bay sediments were iso- lated and
proliferated via several subcultures prior to use for laboratory biodegradation studies. ...

[HTML] Deconstruction created by Lignocellulose interested in Soluble Sugars by the Native and even Designer Cellulosomes

S Moraïs, E Morag, Y Barak, D Goldman, Y Hadar…
... be in charge created by for the focusing on sense made out created by the comprehensive
forensics education a ... Previous SectionNext Section Designer cellulosome technology also has
also been recommended to your indigenous microbial enzymatic destruction created by ...

[HTML] Molecular multiplying associated with polymerases for resistor to environmental inhibitors

C Baar, M d'Abbadie, A Vaisman, ME Arana… - Life Sciences
... associated with plans in medicine and biology running ranging from analysis and diagnostics,
prognostics, forensics to molecular ... using the QiaAmp DNA miniature apparatus (Qiagen) being
for each and every manufacturer's instructions, upcoming microbial standard protocol C ...




So incredibly weird. Is there some site out there that figured out how to scam Google Scholar into linking to them? Anyone seen anything like this before?


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This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter.
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Posted by in google scholar

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20Nov / 2012

Thank you Google Scholar Updates for finding me two new papers to read

Am really liking the Google Scholar Updates system.   Have written about it before: The Tree of Life: Wow - Google Scholar "Updates" a big step forward ... and continue to be impressed.  Today the system suggested two papers for me

Dead on accurate in terms of papers I would be interest in.  #1 is on Drosophila associated microbes and it is a paper from Dmitri Petrov's group: Bacterial diversity associated with Drosophila in the laboratory and in the natural environment.  #2 is on computational normalization of shotgun genome sequence data from Titus Brown and others.  As these are both preprints I almost certainly never would have found them without Google Scholar Updates.

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This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter.
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Posted by in arXiv, google scholar, preprints

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21Sep / 2012

Google Scholar has search by date option – a good thing

Woohoo.  Just discovered a cool (I think new) thing.  Was looking for a link to a new publication of mine.  And I searched Google Scholar


That gets my publications but they are sorted by citation number which alas does not pull up new publications.  So I went to click on the "Since 2012" button I usually click on


And I noticed something I have not noticed before (and that I think must be pretty new):

Woohoo - a full sort by date option.  And so I clicked it and indeed it did work.


This will make Google Scholar much more useful for certain purposes.  This - along with other new features such as the Google Scholar "Updates" system is giving me hope that Google will continue to expand the tools/features of Google Scholar.

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This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter.
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Posted by in google scholar

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11Sep / 2012

Thanks Google Scholar Updates for new article to read .. wish you had an #openaccess only setting

I have a new friend in Google Scholar Updates

I have written about the Updates system before and if you want more information please see this post: The Tree of Life: Wow - Google Scholar "Updates" a big step forward ...

Alas, it is imperfect in my mind for I went to try to read this article and boom - $32 for a day's access


Now I am really wishing Google Scholar had an "show me only open access" articles option.

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This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter.
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Posted by in google scholar

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09Aug / 2012

Wow – Google Scholar "Updates" a big step forward in sifting through the scientific literature

I logged on to Google Scholar a few minutes ago and discovered something very new


This "updates" thing was not there earlier in the day.  So I clicked on the link and got to this page: Scholar Updates: Making New Connections - Google Scholar Blog where James Connor from Google reports
Since Google Scholar launched nearly eight years ago, we’ve been helping people find the research they’re looking for.  But often the spark for discovery comes from making a new connection or looking in a direction that you hadn’t yet considered and that -- before your aha! moment -- you wouldn’t have known to look for.  Today we hope to start fostering these new connections with Scholar Updates. 
We analyze your articles (as identified in your Scholar profile), scan the entire web looking for new articles relevant to your research, and then show you the most relevant articles when you visit Scholar.  We determine relevance using a statistical model that incorporates what your work is about, the citation graph between articles, the fact that interests can change over time, and the authors you work with and cite.  You don’t need to configure updates or enter any queries.  We’ll notify you about new updates by displaying a preview on the homepage and highlighting a bell icon on search results pages: ...
To get article updates relevant to your work, all you need to do is create a public Scholar profile. Article updates will automatically start to appear within a few days. 
Wow.  Completely awesome if it works well.  So, well, let's see if it works well.  For me the system recommends the following

Both have some relevance to me.  The first one is about evolution of a gene family and has a line in the abstract that clearly might have driven the automated suggestion: "Here, we characterize the phylogenomic distribution of the uniporter’s membrane-spanning pore subunit (MCU) and regulatory partner (MICU1)." But, well, I am not too interested in this paper.  Not really my thing.

But paper number 2 seems a bit closer to my heart: REGEN: Ancestral Genome Reconstruction for Bacteria.  And bonus - it is freely available.  And so, well, I read over it.  And it is definitely related to what I do and I probably would not have seen it without this notification.  Cool.

So I give Scholar Updates a 1.5 / 2 score which translates to a 7.5 out of 10.  Not bad.  But could be better.  So I clicked on the "See all Updates" link to see what else was there.  And this was a pleasant surprise.  Here is what I got (showing the first page).


50 papers in all with the "Top" selection selected at the top of the page.  And some even come with a comment like Cites A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea or 

The first 25 of the papers are listed below:
  1. Defining the human microbiome
  2. Measures of phylogenetic differentiation provide robust and complementary insights into microbial communities
  3. VIROME: a standard operating procedure for analysis of viral metagenome sequences
  4. Complete Genome Sequence of Paenibacillus strain Y4. 12MC10, a Novel Paenibacillus lautus strain Isolated from Obsidian Hot Spring in Yellowstone National Park
  5. Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat
  6. Non-contiguous finished genome sequence and description of Clostridium senegalense sp. nov.
  7. Non contiguous-finished genome sequence and description of Bacillus timonensis sp. nov.
  8. Complete genome sequence of Pyrobaculum oguniense
  9. Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NALT)
  10. The Metadata Coverage Index (MCI): A standardized metric for quantifying database metadata richness
  11. Complete genome sequence of the aromatic-degrading deep-terrestrial-subsurface alphaproteobacterium Novosphingobium aromaticivorans type strain (F199 T), …
  12. Complete genome sequence of Thauera aminoaromatica strain MZ1T
  13. Non-contiguous finished genome sequence and description of Anaerococcus vaginalis
  14. Non-contiguous finished genome sequence and description of Alistipes senegalensis sp. nov.
  15. Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton
  16. Predicting kinase-substrate interactions in the era of proteomics
  17. REGEN: Ancestral Genome Reconstruction for Bacteria
  18. Targeted recovery of novel phylogenetic diversity from next-generation sequence data
  19. A call for an international network of genomic observatories (GOs)
  20. Large and linked in scientific publishing
  21. The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome
  22. Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics
  23. Ultrafast clustering algorithms for metagenomic sequence analysis
  24. IMG/M-HMP: A Metagenome Comparative Analysis System for the Human Microbiome Project
  25. Microbiomes
  26. Metagenomic analysis of hadopelagic microbial assemblages thriving at the deepest part of Mediterranean Sea, Matapan‐Vavilov Deep
  27. Distance-Decay diversity patterns of phyllosphere bacteria on Tamarisk trees across the Sonoran Desert
  28. Exposure of Soil Microbial Communities to Chromium and Arsenic Alters Their Diversity and Structure
  29. Reconstruction of Ribosomal RNA Genes from Metagenomic Data
  30. Genome Sequence of the Unclassified Marine Gammaproteobacterium BDW918
  31. Surprising results on phylogenetic tree building methods based on molecular sequences
  32. Road map of the phylum Actinobacteria
  33. Building non-coding RNA families
  34. Bacterial assemblages of the eastern Atlantic Ocean reveal both vertical and latitudinal biogeographic signatures
  35. Metagenomic microbial community profiling using unique clade-specific marker genes
  36. Unlocking the potential of metagenomics through replicated experimental design
  37. Coordinating Environmental Genomics and Geochemistry Reveals Metabolic Transitions in a Hot Spring Ecosystem
  38. Minimizing the average distance to a closest leaf in a phylogenetic tree
  39. Parallel-META: efficient metagenomic data analysis based on high-performance computation
  40. Complete genome sequence of Dehalogenimonas lykanthroporepellens type strain (BL-DC-9T) and comparison to “Dehalococcoides” strains
  41. Complete genome sequence of the orange-red pigmented, radioresistant Deinococcus proteolyticus type strain (MRPT)
  42. Genome sequence of the ocean sediment bacterium Saccharomonospora marina type strain (XMU15T
  43. Genome sequence of the soil bacterium Saccharomonospora azurea type strain (NA-128T)
  44. Evolutionary Diversity of the Mitochondrial Calcium Uniporter
  45. Phylogenetic Clustering Reveals Selective Events Driving the Turnover of Bacterial Community in Alpine Tundra Soils
  46. A comparative evaluation of sequence classification programs
  47. Complete genome sequence of the facultatively anaerobic, appendaged bacterium Muricauda ruestringensis type strain (B1T)
  48. Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1T), reclassification in the genus Sphaerochaeta as …
  49. Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4T)
  50. Permanent draft genome sequence of the gliding predator Saprospira grandis strain Sa g1 (= HR1)
And well, I'll be damned.  I kind of want to read almost all of them.  Son based on the top 50 I would give Scholar Updates a score of something like 47/50 or 9.4 / 10.  Many have complained about the limited developments in Google Scholar over the years but this is definitely a nice development.  I hope it means Google will be putting more effort into other developments.

Now - off to read some papers.  And if you do not have a Google Scholar page - you should definitely think about making one now as this is how you open up this feature.

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UPDATE 1 8/9 1:45 AM

Just noticed that now in the top of the page when I go to Google Scholar there is also now a link to "Updates"



UPDATE 2: 8/9 10 AM - Some other posts about this
UPDATE 3: 8/9 10 AM - Other stuff from around the web about this

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This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter.
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Posted by in google scholar

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