NCATSTranslator / Feedback

A repo for tracking gaps in Translator data and finding ways to fill them.
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'no title available' #681

Closed gglusman closed 3 months ago

gglusman commented 10 months ago

https://ui.test.transltr.io/main/results?l=Pityriasis+Rubra+Pilaris&i=MONDO%3A0100017&t=0&r=94e5d39e&q=cfcdc63b-f49f-4ebd-bda1-c2510bd353f1

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6th reference:

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In PubMed, it does show a title:

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gaurav commented 9 months ago

I'm not sure where this missing title is coming from, but I'm working on adding PubMed and PMC IDs with titles to NodeNorm, to be deployed sometime in Feb. So there should be another source of PMID/PMCID titles in Translator by the next release.

dnsmith124 commented 9 months ago

In this instance it appears the publication server at docmetadata.transltr.io doesn't return a title for PMID:32546899. Here's the request: https://docmetadata.transltr.io/publications?pubids=PMID:32546899&request_id=26394fad-bfd9-4e32-bb90-ef9d5044f593

and the returned data: {"_meta":{"n_results":1,"processing_time_ms":1,"request_id":"26394fad-bfd9-4e32-bb90-ef9d5044f593","timestamp":"2024-01-23T15:5156Z"},"results":{"PMID:32546899":{"abstract":"Purpose: Biotechnological substances (BSs) are strongly relied upon to prevent rejection of transplanted organs, and to treat oncological, allergological, and other inflammatory diseases. Allergic reactions to partly foreign biologics can occur due to their potential immunogenicity. The severity of an immune response to a biological drug may range from no clinical significance to a severe, life-threatening anaphylactic reaction.Methods: Detailed searches were performed on Pubmed, Web of Science, and Google Scholar to include all available publications. In addition, the Food and Drug Administration, the European Medicines Agency, and British Columbia Cancer Agency Drug Manual databases were screened for hypersensitivity reaction (HSR), infusion reaction, injection site reaction, urticaria, and anaphylaxis for individual BSs.Results: Treatment with BSs can cause various types of HSR. These are mentioned in the literature with definitions such as allergic reactions, anaphylactoid reactions, anaphylaxis, HSR, infusion reactions, injection site reactions, cytokine release syndrome, and urticaria. Due to the overlap in signs and symptoms in the reported descriptions, it is not always possible to differentiate these reactions properly according to their pathomechanism. Similarly, many data reported as anaphylaxis actually describe severe anaphylactic reactions (grades III or IV).Conclusion: There is an urgent need for a simpler symptom- or system-based classification and scoring system to create an awareness for HSRs to BSs. A better understanding of the pathophysiology of HSRs and increased clinical experience in the treatment of side effects will provide timely control of unexpected reactions. As a result, immunotherapy with BSs will become safer in the future.Cite this as G\u00fclsen A, Wedi B, Jappe U. Hypersensitivity reactions to biologics (part I): allergy as an important differential diagnosis in complex immune-derived adverse events. Allergo J Int 2020; 29:97-125https://doi.org/10.1007/s40629-020-00126-6.\n","article_title":"","issue":"","journal_abbrev":"Allergo J","journal_name":"Allergo Journal : interdisziplinare Zeitschrift fur Allergologie und Umweltmedizin : Organ der Deutschen Gesellschaft fur Allergie- und Immunitatsforschung","pub_day":"24","pub_month":"Jun","pub_year":"2020","volume":"29"},"not_found":[]}}

The important part of that JSON in our case being: "article_title":""

sierra-moxon commented 9 months ago

@bill-baumgartner - is this a service from TMKP? Is it possible that this publication needs a title update? The UI does eventually show the title and it is available at PubMed.

bill-baumgartner commented 9 months ago

@edgargaticaCU -- would you mind taking a look at this issue? It appears that no title is being returned from the publication metadata service for PMID:32546899.

edgargaticaCU commented 9 months ago

image @bill-baumgartner The API returns an entry for this PMID, but the article_title field is blank. I will track down the original processed file to see if this an upload issue.

sstemann commented 3 months ago

@gglusman I can't recreate this one. can you?

On Prod https://ui.transltr.io/main/results?l=Pityriasis%20Rubra%20Pilaris&i=MONDO:0100017&t=0&r=0&q=9100072c-3864-4b80-86c7-d5c3f4642825

Or On Test https://ui.test.transltr.io/main/results?l=Pityriasis%20Rubra%20Pilaris&i=MONDO:0100017&t=0&r=0&q=11c31e0e-c504-410f-bba4-efc085f4d04b

gglusman commented 3 months ago

Can't really figure out if it was fixed, since CD4 is pretty much absent from the results. Only one result (nevirapine) mentions "increases CD4 counts" in the description, but there's no CD4 node anywhere to be found...

sstemann commented 3 months ago

my only other thought is, would that pub show up for any other connection that might be in the results?

gglusman commented 3 months ago

I think we can safely close this for now. :)