search

pombase / curation

PomBase curation
7 stars 0 forks source link

Duplicate PubMed #3599

Open ValWood opened 9 months ago

ValWood commented 9 months ago

Despite being told that this wasn't important or possible to add forwarding information for deleted identifiers when reported it, PubMed now addresses this issue by providing forwarding links. This is good, It's one thing to cross off the Biocuration Focus group task list (provided we can access this information while loading Canto in some way to make sure we have the correct ID).

Screenshot 2023-10-04 at 08 01 01
ValWood commented 9 months ago

We still have a slight problem, we hadn't identified this one as a duplicate and we have this session (not started) https://curation.pombase.org/pombe/view/object/pub/14098?model=track so now we have all the annotation on the deprecated ID.

For now, I will delete the session associated with PMID: 37288768 I'll continue with approval of PMID:37199119 and we will need to migrate the data from PMID:37199119 to PMID: 37288768

ValWood commented 9 months ago

I wonder why they deleted the first identifier and kept the second one? That's bonkers. People are more likely to be actively using the first identifier before the second one appears.

ValWood commented 9 months ago

We should recheck that we caught ALL the duplicates and triplicates in Canto https://curation.pombase.org/pombe/view/list/triage_duplicated_in_pubmed_publications?model=track (and we have the correct deprecated entry).

ValWood commented 9 months ago

@afg1 something to be aware of...

ValWood commented 9 months ago

Thank you for writing to the PubMed help desk.

If duplicates are introduced, most often when they are resolved the initial PMID is retained. There are cases, such as the one you noted here, when the newer PMID is retained. In this case, PMID 37199119 was deleted because it was an Ahead of Print citation that the publisher did not replace properly.

All changes are included in NLM’s FTP files and may be accessed by your developers (more info here: https://pubmed.ncbi.nlm.nih.gov/download/)

ValWood commented 9 months ago

@kimrutherford is it possible to migrate the annotation from PMID:37199119 to PMID:37288768

kimrutherford commented 8 months ago

is it possible to migrate the annotation from PMID:37199119 to PMID:37288768

No problem. But I'll do it at the weekend when Canto isn't in use.

kimrutherford commented 8 months ago

is it possible to migrate the annotation from PMID:37199119 to PMID:37288768

Done!

ValWood commented 8 months ago

thanks!

ValWood commented 8 months ago

Some time in the future it might be useful to add forwarding links for these IDs https://curation.pombase.org/pombe/view/list/triage_duplicated_in_pubmed_publications?model=track

I will re-add PMID:37199119. to Canto, and put it in here

ValWood commented 8 months ago

I could net re-add it. t might be good to store here so we can keep track of the number of duplicates

ValWood commented 8 months ago

I don't understand what PubMed is doing. Sometimes I got a forwarding link (recently). but there searches just give an error PMID:37199119 https://pubmed.ncbi.nlm.nih.gov/?term=PMID%3A37199119&sort=date

PMID:31579888 https://pubmed.ncbi.nlm.nih.gov/?term=PMID%3A31579888&sort=date

ith no forwarding info

kimrutherford commented 8 months ago

I don't understand what PubMed is doing. Sometimes I got a forwarding link (recently). but there searches just give an error

I found that if you have a direct link that uses the old ID, it redirects to the new ID: https://pubmed.ncbi.nlm.nih.gov/37199119

But if you search for the old ID you get nothing.

kimrutherford commented 8 months ago

Hi Val.

I've had a look in Canto for publications with identical titles (after ignoring the full spot at the end). The table is below. The columns are:

A few have re-directions at PubMed:

Most don't though:

This publication:

is an erratum for:

It's not helpful for them to have the same title.

These have the same title and authors, but a different citation and PMID:

(That cases seems familiar)

duplicate_pubs_with_sessions.tsv.txt

pmids pmid_of_session session_id title
PMID:12901373,PMID:12727899 Parallel evolution by gene duplication in the genomes of two unicellular fungi
PMID:1482118,PMID:7011176 Genetics of the fission yeast Schizosaccharomyces pombe
PMID:21979813,PMID:28673925 PMID:21979813 f07cbe80a4008b28 Acetylation regulates monopolar attachment at multiple levels during meiosis I in fission yeast
PMID:26821940,PMID:31748542 Boolean Models of Biological Processes Explain Cascade-Like Behavior
PMID:27327046,PMID:28084030 PMID:27327046 8bbf965b2fdf46b6 Use of a fluoride channel as a new selection marker for fission yeast plasmids and application to fast genome editing with CRISPR/Cas9
PMID:29414716,PMID:29694880 Modeling the Dynamics of Cdc42 Oscillation in Fission Yeast
PMID:30647105,PMID:33575752 PMID:30647105 552b014f7404cd32 Comparative Genomic Screen in Two Yeasts Reveals Conserved Pathways in the Response Network to Phenol Stress
PMID:31278118,PMID:33954735,PMID:33954710 PMID:31278118 edfee9c20ff8ca78 Cohesin Impedes Heterochromatin Assembly in Fission Yeast Cells Lacking Pds5
PMID:31405990,PMID:33954475,PMID:33954444 PMID:31405990 4e543d94b99bb08c RNA-DNA Hybrids Support Recombination-Based Telomere Maintenance in Fission Yeast
PMID:31511300,PMID:33954703,PMID:33954671 PMID:31511300 f621d80f3fce5599 Diverse DNA Sequence Motifs Activate Meiotic Recombination Hotspots Through a Common Chromatin Remodeling Pathway
PMID:31575705,PMID:31579888 PMID:31575705 6d4a9d65ed297cda Chromatin remodeler Fft3 plays a dual role at blocked DNA replication forks
PMID:32917738,PMID:33830259 A Fully Functional ROP Fluorescent Fusion Protein Reveals Roles for This GTPase in Subcellular and Tissue-Level Patterning
PMID:8736869,PMID:8879047 PMID:8879047 9ff9e4a1410473cd Maturation of Krp1, an endopeptidase from the fission yeast Schizosaccharomyces pombe
PMID:8741848,PMID:8589453 Nucleolar accumulation of poly (A)+ RNA in heat-shocked yeast cells: implication of nucleolar involvement in mRNA transport
PMID:9439701,PMID:9127201 Identification of preussin as a selective inhibitor for cell growth of the fission yeast ts mutants defective in Cdc2-regulatory genes
kimrutherford commented 8 months ago

Related issue:

ValWood commented 8 months ago

Blimey!

ValWood commented 8 months ago

wrong organism, ignore:

|PMID:10865904,PMID:29265614| | |Histidine kinase, two-component signal transduction proteins of Candida albicans and the pathogenesis of candidosis
|PMID:16957386,PMID:23007516| | |Transgene-like animal models using intronic microRNAs |

ValWood commented 8 months ago

Erratum (flagged)

|PMID:9064503,PMID:8524294|PMID:8524294 |d37836a2104d53bc |Schizosaccharomyces pombe skp1+ encodes a protein kinase related to mammalian glycogen synthase kinase 3 and complements a cdc14 cytokinesis mutant |

ValWood commented 8 months ago

Independent publications |PMID:8167016,PMID:24467403| | |The yeast actin cytoskeleton | |PMID:19563122,PMID:25916706| | |Measuring DNA content by flow cytometry in fission yeast | |PMID:19563123,PMID:25916703| | |Microscopy techniques to examine DNA replication in fission yeast | |PMID:19563126,PMID:25916707| | |Incorporation of thymidine analogs for studying replication kinetics in fission yeast |

ValWood commented 8 months ago

OneBioarchive |PMID:36945401,PMID:37556551| | |The minimal intrinsic stochasticity of constitutively expressed eukaryotic genes is sub-Poissonian | |PMID:36945624,PMID:37200372|PMID:37200372 |7ad9eb5a73f1bab1 |Comprehensive mutational analysis of the checkpoint signaling function of Rpa1/Ssb1 in fission yeast | |PMID:36993237,PMID:37158439|PMID:37158439 |5e4169b314b92367 |The fission yeast cytokinetic ring component Fic1 promotes septum formation | |PMID:37131752,PMID:37610834|PMID:37610834 |432df2300582f190 |Design principles of Cdr2 node patterns in fission yeast cells | |PMID:37163016,PMID:37531259|PMID:37531259 |0ae5e45bd4264f63 |Membrane binding of endocytic myosin-1s is inhibited by a class of ankyrin repeat proteins | |PMID:37205432,PMID:37725645|PMID:37725645 |7f1dc29239d93d50 |Distinct regions of the kinesin-5 C-terminal tail are essential for mitotic spindle midzone localization and sliding force | |PMID:37546978,PMID:37815455|PMID:37815455 |2f93fe0b9007bce3 |Characterization of Pik1 function in fission yeast reveals its conserved role in lipid synthesis and not cytokinesis | |PMID:36778333,PMID:37099380|PMID:37099380 |0083e32788245bc8 |Microtubule competition and cell growth recenter the nucleus after anaphase in fission yeast |

ValWood commented 8 months ago

Duplicated in Pubmed (triage status) |PMID:34279633,PMID:34402513|PMID:34402513 |0f10611fa56323c0 |Phosphorylation in the intrinsically disordered region of F-BAR protein Imp2 regulates its contractile ring recruitment | |PMID:33954563,PMID:33954521| | |F-BAR Cdc15 Promotes Cdc42 Activation During Cytokinesis and Cell Polarization in Schizosaccharomyces pombe
|PMID:31345994,PMID:33954739,PMID:33954709|PMID:31345994 |80bab75459a4ce45 |Histone H2B Ubiquitylation Regulates Histone Gene Expression by Suppressing Antisense Transcription in Fission Yeast |

kimrutherford commented 8 months ago

Hi Val. I found two more duplicates. I forgot to ignore white-space when comparing titles. In both of these cases there was an extra space before the full-stop in the title of one of the entries.

The second one here is the one that's still in PubMed:

This is the wrong organism so no problem: