<p>The idea for this code is to first convert PIDs to PMCIDs, then run the <code>tidypmc</code> in a loop over the PMCIDs. The only problem is that <code>tidypmc</code> failed to retrieve tables from most of the IDs in your example list.</p>
<pre><code>library(tidyverse)
library(tidypmc)
library(httr)
library(jsonlite)
example_pids &lt;- c(30024784, 30555165, 30510081, 31688884, 31516032, 28588019, 29286103) %&gt;% as.character()

#-- Convert to PMC ids
convertPIDtoPMCID &lt;- function(pids) {
    #-------- Make API request
    pids4query &lt;- paste(pids, collapse = &quot;%0D%0A&quot;)
    idconv_req &lt;- paste0(&quot;https://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0/?ids=&quot;, pids4query, &quot;&amp;idtype=pmid&amp;format=json&amp;versions=no&amp;showaiid=no&amp;tool=&amp;email=&amp;.submit=Submit&quot;)
    pids_json &lt;- GET(idconv_req) %&gt;% content(&quot;text&quot;) %&gt;% fromJSON()
    #-------- Get info from JSON
    pid2pmc &lt;- pids_json<span class="math-container">$records %&gt;% 
        select(pmcid, pmid) %&gt;% 
        as.data.frame()
    rownames(pid2pmc) &lt;- pid2pmc$</span>pmid
    pmcids &lt;- pmcids &lt;- pid2pmc[pids, &quot;pmcid&quot;]
    return(pmcids)
}
example_pmcids &lt;- convertPIDtoPMCID(example_pids)

#-- Try to get data with tidypmc
pub_tables &lt;- lapply(example_pmcids, function(pmc_id) {
    message(&quot;-- Trying &quot;, pmc_id, &quot;...&quot;)
    doc &lt;- tryCatch(pmc_xml(pmc_id), 
                    error = function(e) {
                        message(&quot;------ Failed to recover PMCID&quot;)
                        return(NULL)
                        })
    if(!is.null(doc)) { 
        #-- If succeed, try to get table
        tables &lt;- pmc_table(doc)
        if(!is.null(tables)) {
            #-- If succeed, try to get table name
            table_caps &lt;- pmc_caption(doc) %&gt;%
                filter(tag == &quot;table&quot;)
            names(tables) &lt;- paste(table_caps<span class="math-container">$label, table_caps$</span>text, sep = &quot; - &quot;)
        }
        return(tables) 
    } else {
        #-- If fail, return NA
        return(NA)
    }
})
names(pub_tables) &lt;- example_pids

#-- Inspect results
pub_tables<span class="math-container">$`30555165`$</span>`Table 1 - Patient demographic and baseline characteristics`
pub_tables<span class="math-container">$`29286103`$</span>`Table I - Sample summary.`
</code></pre>
<p>Tables will require quite a bit of tidying after this. Good luck!</p>

CC BY-SA 4.0
2020-07-27T19:20:05.190Z
https://github.com/ropensci/tidypmc/issues/3 this answer from the library developer
kcm
CC BY-SA 4.0
2020-07-27T21:29:46.830Z
`b <-epmc_search(query = 'acute myeloid leukemia drug studies',output = 'parsed',limit = 200)`
    `a <- b %>% select(pmid,pmcid)`
`a <- a[complete.cases(a),]`
  `c <- a$pmcid`
   `Error in names(tables) <- paste(table_caps$label, table_caps$text, sep = " - ") : 
      'names' attribute [4] must be the same length as the vector [2]`                                           Im getting this error when i run the pub_tables chunk
kcm
CC BY-SA 4.0
2020-07-28T07:26:53.133Z
after multiple trial and errors when I did this       `#names(tables) <- paste(table_caps$label, table_caps$text, sep = " - ")` i get no error I do see a final list why is it so?
kcm
CC BY-SA 4.0
2020-07-28T09:48:11.943Z
That line is just for embellishment, you shouldn't have a problem removing it. It adds the title of the table. But it might fail if the metadata doesn't have the table title. So feel free to remove it.
csgroen
CC BY-SA 4.0
2020-07-28T10:56:48.940Z
this happen when i don't learn R properly i was breaking my head few hours .thank you for the clarification
kcm
CC BY-SA 4.0
2020-07-28T15:44:36.920Z
Most publications with a Pubmed ID are not open access and you cannot mine the text, so be sure to filter results using OPEN_ACCESS:Y in Europe PMC
Chris S.
CC BY-SA 4.0
2020-07-29T08:06:09.847Z
@csgroen is there any way simple way to save the pub_tables which is a list into tabular form ?
kcm
CC BY-SA 4.0
2020-07-30T08:00:11.837Z
@krushnachChandra Tabular data represents m observations of n variables. The issue here is that each table has different variables and observations. How can you join tables that have different columns and different rows? You can't. That's why we get a list.
csgroen
CC BY-SA 4.0
2020-07-30T09:59:30.583Z
@csgroen I found a a temporary way just tot store https://stackoverflow.com/questions/56374683/write-list-of-lists-to-separate-csv-files
 yes you are right we can;'t join unless there is some variable which is common across tables. I'm exploring Chris way where he combined them into data-frame which can probably the parsed
kcm
CC BY-SA 4.0
2020-07-27T15:23:35.993Z
2020-07-27T15:23:35.993Z
csgroen
<p>I'm trying to use this <a href="https://ropensci.org/tutorials/europepmc_tutorial/" rel="nofollow noreferrer">europmc r libray</a> where I have a list of pmids to look for. I tried with pubtator but its bit complicated.In Europmc i can all the annotated terms etc.</p>
<pre><code>library(&quot;europepmc&quot;)

example list of PMIDS
30024784
30555165
30510081
31688884
31516032
28588019
29286103
</code></pre>
<p>Now what I'm doing is looking each ID using epmc_details function which is not the way i would do if i have to look for hundreds.</p>
<pre><code>epmc_details(ext_id = '30510081')
</code></pre>
<p>I have to question how can I run the epmc_details in a loop or some other way where i can look for PMIDS one by one and save the result in a data frame.</p>
<p>The epmc_details is returned as a list. The structure of the list is as such</p>
<pre><code>[1] &quot;basic&quot;           &quot;author_details&quot;  &quot;journal_info&quot;    &quot;ftx&quot;             &quot;chemical&quot;        &quot;mesh_topic&quot;      &quot;mesh_qualifiers&quot;
[8] &quot;comments&quot;        &quot;grants&quot;    
</code></pre>
<p>I would only like to save basic,chemical,mesh_topic,mesh_qualifiers in one data frame.</p>
<p>For example if my first id is this <code>30510081</code> the dataframe should have first column as my ID which is basically <code>basic[1]</code>and rest of the information appended to the next columns.</p>
<p>such as</p>
<pre><code> ID chemical mesh_qualifiers mesh_topic gene 
</code></pre>
<p>Any suggestion or help would be really and highly appreciated</p>
<p>I was looking at europmc site through the browser</p>
<p>this was one of my <a href="https://europepmc.org/article/MED/32700753" rel="nofollow noreferrer">query</a></p>
<p>when i highlight the keyterms i do see in the abstract itself all the keyterms are getting annotated but when i do the same query search through R I do see empty results as such why there is a difference?</p>
<pre><code>$chemical
# A tibble: 0 x 0

$mesh_topic
# A tibble: 0 x 0

$mesh_qualifiers
# A tibble: 0 x 0
</code></pre>
<p>I found better way of getting data from pubmed using the <a href="https://docs.ropensci.org/tidypmc/index.html" rel="nofollow noreferrer">tidypmc</a> library.</p>
<pre><code>library(tidypmc)
doc &lt;- pmc_xml(&quot;PMC6365492&quot;)
doc
txt &lt;- pmc_text(doc)
txt

count(txt, &quot;section&quot;)

cap1 &lt;- pmc_caption(doc)
filter(cap1, sentence == 1)

tab1 &lt;- pmc_table(doc)

sapply(tab1, nrow)

tab1[[1]]
attributes(tab1[[2]])

collapse_rows(tab1, na.string=&quot;-&quot;)

library(tibble)
x &lt;- xml_name(xml_find_all(doc, &quot;//*&quot;))
tibble(tag=x) %&gt;% count(&quot;tag&quot;)

library(tidytext)
x1 &lt;- unnest_tokens(txt, word, text) %&gt;%
  anti_join(stop_words) %&gt;%
  filter(!word %in% 1:100)
#  Joining, by = &quot;word&quot;
#filter(x1, str_detect(section, &quot;Case description&quot;)) 


filter(x1, str_detect(section, &quot;Results&quot;))
count(a$word)

tbls &lt;- pmc_table(doc)
map_int(tbls, nrow)

tbls[[1]]

collapse_rows(tbls, na.string=&quot;-&quot;)
</code></pre>
<p>But if i understand it can use one PMC id at a time. Again keeping my original question how can i put this in a loop to query lets say i have 100 PMCID and get it result and store in a dataframe.</p>
<p>After using tidypmc i found that i parse all the publication based on attributes or tags. Such as title,abstract, results etc etc.</p>
<p>Lets say I'm interested in the table tags information where they have metadata of patients as well as others.So if a paper contain multiple tables I would like to store each of them in a data-frame under the respective publication.Since I have multiple IDs to search and do the save as above mentioned. How to put this through a loop or can it be done without using loop ?</p>
<p>Any suggestion or help would be really appreciated as always.</p>

CC BY-SA 4.0
2020-07-26T08:55:49.003Z
I think the content of that article are not available in pubmed, you can only download a pdf through some link.. again.. it's my guess.. maybe if you do more you will see this repeats itself
StupidWolf
CC BY-SA 4.0
2020-07-27T10:56:44.170Z
@StupidWolf i found tidypmc is better but yes it will only look for article which has PMCID . I have updated my question and query, I would be glad if you can have a look and give your suggestion.
kcm
<r><public-databases><parsing>
europmc and tidypmc R library for extracting or making metadata from publication
# europmc and tidypmc R library for extracting or making metadata from publication

(Asked by: username_0 on 2020-07-24)

I'm trying to use this europmc r libray where I have a list of pmids to look for. I tried with pubtator but its bit complicated.In Europmc i can all the annotated terms etc.
library("europepmc")

example list of PMIDS
30024784
30555165
30510081
31688884
31516032
28588019
29286103

Now what I'm doing is looking each ID using epmc_details function which is not the way i would do if i have to look for hundreds.
epmc_details(ext_id = '30510081')

I have to question how can I run the epmc_details in a loop or some other way where i can look for PMIDS one by one and save the result in a data frame.
The epmc_details is returned as a list. The structure of the list is as such
[1] "basic"           "author_details"  "journal_info"    "ftx"             "chemical"        "mesh_topic"      "mesh_qualifiers"
[8] "comments"        "grants"    

I would only like to save basic,chemical,mesh_topic,mesh_qualifiers in one data frame.
For example if my first id is this 30510081 the dataframe should have first column as my ID which is basically basic[1]and rest of the information appended to the next columns.
such as
 ID chemical mesh_qualifiers mesh_topic gene 

Any suggestion or help would be really and highly appreciated
I was looking at europmc site through the browser
this was one of my query
when i highlight the keyterms i do see in the abstract itself all the keyterms are getting annotated but when i do the same query search through R I do see empty results as such why there is a difference?
$chemical
# A tibble: 0 x 0

$mesh_topic
# A tibble: 0 x 0

$mesh_qualifiers
# A tibble: 0 x 0

I found better way of getting data from pubmed using the tidypmc library.
library(tidypmc)
doc <- pmc_xml("PMC6365492")
doc
txt <- pmc_text(doc)
txt

count(txt, "section")

cap1 <- pmc_caption(doc)
filter(cap1, sentence == 1)

tab1 <- pmc_table(doc)

sapply(tab1, nrow)

tab1[[1]]
attributes(tab1[[2]])

collapse_rows(tab1, na.string="-")

library(tibble)
x <- xml_name(xml_find_all(doc, "//*"))
tibble(tag=x) %>% count("tag")

library(tidytext)
x1 <- unnest_tokens(txt, word, text) %>%
  anti_join(stop_words) %>%
  filter(!word %in% 1:100)
#  Joining, by = "word"
#filter(x1, str_detect(section, "Case description")) 


filter(x1, str_detect(section, "Results"))
count(a$word)

tbls <- pmc_table(doc)
map_int(tbls, nrow)

tbls[[1]]

collapse_rows(tbls, na.string="-")

But if i understand it can use one PMC id at a time. Again keeping my original question how can i put this in a loop to query lets say i have 100 PMCID and get it result and store in a dataframe.
After using tidypmc i found that i parse all the publication based on attributes or tags. Such as title,abstract, results etc etc.
Lets say I'm interested in the table tags information where they have metadata of patients as well as others.So if a paper contain multiple tables I would like to store each of them in a data-frame under the respective publication.Since I have multiple IDs to search and do the save as above mentioned. How to put this through a loop or can it be done without using loop ?
Any suggestion or help would be really appreciated as always.

**Tags:** r, public-databases, parsing
> **Comments:**
> **username_1**: I think the content of that article are not available in pubmed, you can only download a pdf through some link.. again.. it's my guess.. maybe if you do more you will see this repeats itself  
> **username_0**: @StupidWolf i found tidypmc is better but yes it will only look for article which has PMCID . I have updated my question and query, I would be glad if you can have a look and give your suggestion.  

---

## 1 answers

### Answer by username_2 on 2020-07-27. Score: 3 | Accepted answer

The idea for this code is to first convert PIDs to PMCIDs, then run the tidypmc in a loop over the PMCIDs. The only problem is that tidypmc failed to retrieve tables from most of the IDs in your example list.
library(tidyverse)
library(tidypmc)
library(httr)
library(jsonlite)
example_pids <- c(30024784, 30555165, 30510081, 31688884, 31516032, 28588019, 29286103) %>% as.character()

#-- Convert to PMC ids
convertPIDtoPMCID <- function(pids) {
    #-------- Make API request
    pids4query <- paste(pids, collapse = "%0D%0A")
    idconv_req <- paste0("https://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0/?ids=", pids4query, "&idtype=pmid&format=json&versions=no&showaiid=no&tool=&email=&.submit=Submit")
    pids_json <- GET(idconv_req) %>% content("text") %>% fromJSON()
    #-------- Get info from JSON
    pid2pmc <- pids_json$records %>% 
        select(pmcid, pmid) %>% 
        as.data.frame()
    rownames(pid2pmc) <- pid2pmc$pmid
    pmcids <- pmcids <- pid2pmc[pids, "pmcid"]
    return(pmcids)
}
example_pmcids <- convertPIDtoPMCID(example_pids)

#-- Try to get data with tidypmc
pub_tables <- lapply(example_pmcids, function(pmc_id) {
    message("-- Trying ", pmc_id, "...")
    doc <- tryCatch(pmc_xml(pmc_id), 
                    error = function(e) {
                        message("------ Failed to recover PMCID")
                        return(NULL)
                        })
    if(!is.null(doc)) { 
        #-- If succeed, try to get table
        tables <- pmc_table(doc)
        if(!is.null(tables)) {
            #-- If succeed, try to get table name
            table_caps <- pmc_caption(doc) %>%
                filter(tag == "table")
            names(tables) <- paste(table_caps$label, table_caps$text, sep = " - ")
        }
        return(tables) 
    } else {
        #-- If fail, return NA
        return(NA)
    }
})
names(pub_tables) <- example_pids

#-- Inspect results
pub_tables$`30555165`$`Table 1 - Patient demographic and baseline characteristics`
pub_tables$`29286103`$`Table I - Sample summary.`

Tables will require quite a bit of tidying after this. Good luck!

> **Comments:**
> **username_0**: https://github.com/ropensci/tidypmc/issues/3 this answer from the library developer  
> **username_0**: `b <-epmc_search(query = 'acute myeloid leukemia drug studies',output = 'parsed',limit = 200)`     `a <- b %>% select(pmid,pmcid)` `a <- a[complete.cases(a),]`   `c <- a$pmcid`    `Error in names(tables) <- paste(table_caps$label, table_caps$text, sep = " - ") :        'names' attribute [4] must be the same length as the vector [2]`                                           Im getting this error when i run the pub_tables chunk  
> **username_0**: after multiple trial and errors when I did this       `#names(tables) <- paste(table_caps$label, table_caps$text, sep = " - ")` i get no error I do see a final list why is it so?  
> **username_2**: That line is just for embellishment, you shouldn't have a problem removing it. It adds the title of the table. But it might fail if the metadata doesn't have the table title. So feel free to remove it.  
> **username_0**: this happen when i don't learn R properly i was breaking my head few hours .thank you for the clarification  
> **username_3**: Most publications with a Pubmed ID are not open access and you cannot mine the text, so be sure to filter results using OPEN_ACCESS:Y in Europe PMC  
> **username_0**: @csgroen is there any way simple way to save the pub_tables which is a list into tabular form ?  
> **username_2**: @krushnachChandra Tabular data represents m observations of n variables. The issue here is that each table has different variables and observations. How can you join tables that have different columns and different rows? You can't. That's why we get a list.  
> **username_0**: @csgroen I found a a temporary way just tot store https://stackoverflow.com/questions/56374683/write-list-of-lists-to-separate-csv-files  yes you are right we can;'t join unless there is some variable which is common across tables. I'm exploring Chris way where he combined them into data-frame which can probably the parsed  

---

