Notes
user@computer:~$represents an example terminal prompt name. Actual command/argument input is after the$.- Replace
name@xx.eduwith your email address.\followed by>on the next line represents continued terminal input. You will need to delete the>symbol in order to run the scripts as a copy/paste into terminal.- You should validate your own EDirect scripts and results as there may be unintentional mistakes in these recipes. A convenient method is to compare your EDirect results to the NCBI Web interface search results: https://www.ncbi.nlm.nih.gov/.
Description: Search for a CID in the PubChem Compound Database and retrieve related PubMed linked references.
In the below script, we use the esearch function to query the PubChem Compound database (pccompound) for CID 174076 within the Compound ID field, [uid]. The esearch results are then piped to elink finding related PubMed citations via the Entrez link pccompound_pubmed. Finally, we retrieve the results with efetch in XML format and extract out some bibliographic reference information using the xtract function.
user@computer:~$ esearch -email name@xx.edu -db pccompound -query 174076[uid] | \
> elink -target pubmed -name pccompound_pubmed | \
> efetch -format xml | \
> xtract -pattern PubmedArticle -element MedlineCitation/PMID -first Author/LastName \
> Author/Initials ISOAbbreviation PubDate/Year Volume Issue MedlinePgn
22957575 Gabl S J Chem Phys 2012 137 9 094501
22868451 Zhang Y Phys Chem Chem Phys 2012 14 35 12157-64
22859056 Malberg F Phys Chem Chem Phys 2012 14 35 12079-82
22852554 Zhang Y J Phys Chem B 2012 116 33 10036-48
22662183 Zhang BB PLoS ONE 2012 7 5 e37641
...tested on 2021.01.26, EDirect 14.4, total count was 102.
Description: Search for CID in PubChem Compound Database, find related PubMed citations, then only retrieve references from a specific journal.
We can filter elink results with efilter to only include PubMed citations (Entrez linked via pccompound_pubmed) to the CID but also matching a specific PubMed query. For example, if we are only interested in linked Phys Chem Chem Phys references to CID 174076, we can use the journal field [JOUR] in an efilter query:
user@computer:~$ esearch -email name@xx.edu -db pccompound -query 174076[uid] | \
> elink -target pubmed -name pccompound_pubmed | \
> efilter -query "Phys Chem Chem Phys"[JOUR] | \
> efetch -format xml | \
> xtract -pattern PubmedArticle -element MedlineCitation/PMID -first Author/LastName \
> Author/Initials ISOAbbreviation PubDate/Year Volume Issue MedlinePgn
22868451 Zhang Y Phys Chem Chem Phys 2012 14 35 12157-64
22859056 Malberg F Phys Chem Chem Phys 2012 14 35 12079-82
22451012 Sillars FB Phys Chem Chem Phys 2012 14 17 6094-100
21643581 Pensado AS Phys Chem Chem Phys 2011 13 30 13518-26
21643580 Schröder C Phys Chem Chem Phys 2011 13 26 12240-8
...tested on 2021.01.26, EDirect 14.4, total count was 11.
Description: Search for a CID in PubChem Compound, find related PubMed records via MeSH, and retrieve only references that contain the MeSH subheading "chemical synthesis".
This is my favorite literature search: start with a PubChem CID and then find PubMed literature related to its synthesis. Similarly to the search above, we can filter out references using an efilter query for 'chemical synthesis' as a MeSH subheading [SUBH]. Note that we used the pccompound_pubmed_mesh Entrez link as the elink target name here.
user@computer:~$ esearch -email name@xx.edu -db pccompound -query 94257[uid] | \
> elink -target pubmed -name pccompound_pubmed_mesh | \
> efilter -query "chemical synthesis"[SUBH] | \
> efetch -format xml | \
> xtract -pattern PubmedArticle -element MedlineCitation/PMID ArticleTitle \
> ISOAbbreviation PubDate/Year
28463562 Enantioselective Chemical Syntheses of the Furanosteroids (-)-Viridin and (-)-Viridiol. J. Am. Chem. Soc. 2017
23040731 Viridin analogs derived from steroidal building blocks. Bioorg. Med. Chem. Lett. 2012
22849426 Synthetic studies on furanosteroids: construction of the viridin core structure via Diels-Alder/retro-Diels-Alder and vinylogous Mukaiyama aldol-type reaction. J. Org. Chem. 2012
19644878 Abrogation of antibody-induced arthritis in mice by a self-activating viridin prodrug and association with impaired neutrophil and endothelial cell function. Arthritis Rheum. 2009
19572524 Pentacyclic furanosteroids: the synthesis of potential kinase inhibitors related to viridin and wortmannolone. J. Org. Chem. 2009
...tested on 2021.01.26, EDirect 14.4, total count was 8.
Description: Search for a CID in PubChem Compound, find related PubMed citations and related PubMed citations via MeSH.
It appears that you can combine elink queries, with either the same Entrez link or a different Entrez link, but within the same database. For example, if we want to retrieve PubMed literature related to PubChem CID 174076 for both the pccompound_pubmed and pccompound_pubmed_mesh Entrez links in one dataset, we combine two separate elink queries with an OR operator:
user@computer:~$ esearch -email name@xx.edu -db pccompound -query 174076[uid] | \
> elink -target pubmed -name pccompound_pubmed -label pubmed_cit | \
> esearch -email name@xx.edu -db pccompound -query 174076[uid] | \
> elink -target pubmed -name pccompound_pubmed_mesh -label pubmed_mesh_cit | \
> esearch -query "(#pubmed_cit) OR (#pubmed_mesh_cit)" | \
> efetch -format xml | \
> xtract -pattern PubmedArticle -element MedlineCitation/PMID -first Author/LastName \
> Author/Initials ISOAbbreviation PubDate/Year Volume Issue MedlinePgn
32231037 Babicka M Molecules 2020 25 7
31931064 Love SA Int J Biol Macromol 2020 147 569-575
31818016 Wang F Int J Mol Sci 2019 20 24
31814059 Weber AL Orig Life Evol Biosph 2019 49 4 199-211
31675504 Gomez-Herrero E Ecotoxicol Environ Saf 2020 187 109836
31520950 Pal S Ecotoxicol Environ Saf 2019 184 109634
...tested on 2021.01.26, EDirect 14.4, total count was 317.
Description: Search for a PubChem Substance Data Source Depositor, find related same PubChem Compounds, and then retrieve related PubMed references linked via publisher.
In the below script, we first search the PubChem Substance (pcsubstance) database using esearch for the data source depositor Nature Communications. We can use the Current Source Name [CSN] field for this query. Note that an underscore is put in place of the space in the query. This syntax is important for searching in PubChem with the EDirect esearch function. After esearch, we pipe the results into elink twice, first finding related PubChem Compounds via the pcsubstance_pccompound_same Entrez link, and then using this new result list to find related PubMed publisher deposited citations from the pccompound_pubmed_publisher Entrez link. Finally, similarly to previous searches, we use a combination of efetch and xtract to retrieve selected data:
user@computer:~$ esearch -email name@xx.edu -db pcsubstance -query "nature_communications"[CSN] | \
> elink -target pccompound -name pcsubstance_pccompound_same | \
> elink -target pubmed -name pccompound_pubmed_publisher | \
> efetch -format xml |
> xtract -pattern PubmedArticle -element MedlineCitation/PMID -first Author/LastName Author/Initials \
> ISOAbbreviation PubDate/Year Volume Issue MedlinePgn
26673265 Gilbert ZW Nat Chem 2016 8 1 63-8
25424885 Yan T Nat Commun 2014 5 5602
25422853 Vaidya AB Nat Commun 2014 5 5521
25382411 Dommerholt J Nat Commun 2014 5 5378
25382259 Wang B Nat Commun 2014 5 5354
...tested on 2021.01.26, EDirect 14.4, total count was 101.
Description: Search for a PubChem Substance Data Source Depositor, find related same PubChem Compounds, and then retrieve related PubMed PMIDs linked via publisher.
Building upon the previous search, if needed, it is possible to obtain individual relationships of the CIDs to PubMed IDs (CID <--> PMID). We can do this using the -cmd neighbor option in elink:
user@computer:~$ esearch -email name@xx.edu -db pcsubstance -query "nature_communications"[CSN] | \
> elink -target pccompound -name pcsubstance_pccompound_same | \
> elink -target pubmed -name pccompound_pubmed_publisher -cmd neighbor | \
> xtract -pattern LinkSet -element Id
146033657 24398593
136286496
136264969 24177669
136264968 24177669
136262920 23385592
136262919 23385592
136247006 24457545
136247005 24457545
136247004 24457545
136247003 24457545
136219971
135922679 22027590
91868204 23764831
...tested on 2021.01.26, EDirect 14.4, total count was 1594 (returns all CIDs, not all have linked PMIDs).
The first column contains the PubChem CIDs and the second column contains the linked PMIDs. Additional linked PMIDs are placed in subsequent columns when available.
Description: Search for a PubChem CID in PubChem Compound, then retrieve related PubChem active BioAssay data.
To retrieve BioAssay results labeled as 'Active' that are linked to a CID, we can use the elink function with the PubChem BioAssay (pcassay) database via Entrez link pccompound_pcassay_active. This is followed by efetch and xtract. In this particular example, we extracted the AID, CurrentSourceName, AssayName, ActiveSidCount, and TargetCount:
user@computer:~$ esearch -email name@xx.edu -db pccompound -query "6303"[uid] | \
> elink -target pcassay -name pccompound_pcassay_active | \
> efetch -format docsum | \
> xtract -pattern DocumentSummary -element AID CurrentSourceName AssayName ActiveSidCount TargetCount
1255098 ChEMBL Inhibition of TLR4-mediated NF-kappaB signaling pathway in BALB/c mouse RAW264.7 cells assessed as suppression of LPS-stimulated PGE2 production at 1 to 10 ug/ml preincubated for 1 hr followed by LPS challenge measured after 6 hrs by immunoblot analysis 1 1
1255092 ChEMBL Inhibition of TLR4-mediated NF-kappaB signaling pathway in BALB/c mouse RAW264.7 cells assessed as suppression of LPS-stimulated TNF-alpha production at 1 to 10 ug/ml preincubated for 1 hr followed by LPS challenge measured after 6 hrs by immunoblot analysis 1 1
751324 ChEMBL Inhibition of NFkappaB p65 nuclear translocation in mouse RAW264.7 cells after 24 hrs by DAPI staining-based laser confocal immunofluorescent microscopic analysis 1 1
...tested on 2021.01.26, EDirect 14.4, total count was 47.
Description: Search for a PubChem CID in PubChem Compound Database, find related compounds with same connectivity, then retrieve related AIDs for each CID.
It is possible to obtain individual relationships of the CIDs to BioAssay AIDs (CID <--> AID). We can do this using the -cmd neighbor option in elink. Note that we first found related compounds with same connectivity using the Entrez link pccompound_pccompound_sameconnectivity_pulldown. This step was followed by the pccompound_pcassay_active Entrez link in the PubChem BioAssay database to retrieve AID links to the CIDs. We used the 'Active' assay links here. There are also other Entrez PubChem Compound assay links such as inactive, pccompound_pcassay_inactive.
user@computer:~$ esearch -email name@xx.edu -db pccompound -query "6303"[uid] | \
> elink -target pccompound -name pccompound_pccompound_sameconnectivity_pulldown | \
> elink -target pcassay -name pccompound_pcassay_active -cmd neighbor | \
> xtract -pattern LinkSet -element Id
...
...
6335098
688425
451875 1347103 1296009 2551 2546
248010 687016 652245 651719 177 175 173 171 169 167 165 163 161 159 157 155 153 149 147
6303 1346987 1259407 1255098 1255092 1207585 1207584 1207579 1207578 1207577 1207576 1167619 1159565 1159562 1159559 1159557 1065715 1065714 1065710 1065706 1065697 1065696 1065695 1065713 1065705 1065699 751324 686979 686978 651820 652245 651719 602346 602250 588511 493002 463218 463212 416870 416743 216185 86858 81069 32353 32352 31719 31718 2467tested on 2021.01.26, EDirect 14.4, total count was 24 CIDs (not all have associated AIDs).
Description: Search for a PubMed article ID (PMID), then retrieve related PubChem Compounds.
In the below script, we first use esearch to query PubMed for the article ID 29407984 in the [PMID] field. This result is then piped into elink to retrieve linked compounds in the PubChem Compound database (pubmed_pccompound). In this case, there was one compound and we used efetch to retrieve the CID record as docsum XML, followed by xtraxt to extract out the IsomericSmiles, CID, and InChIKey values.
user@computer:~$ esearch -email name@xx.edu -db pubmed -query "29407984"[PMID] | \
> elink -target pccompound -name pubmed_pccompound | \
> efetch -format docsum | \
> xtract -pattern DocumentSummary -element IsomericSmiles CID InChIKey
C1CC1N2C=C(C(=O)C3=CC(=C(C=C32)N4CCNCC4)F)C(=O)O 2764 MYSWGUAQZAJSOK-UHFFFAOYSA-N
tested on 2021.01.26, EDirect 14.4, total count was 1.
Description: Search for a PubMed article ID (PMID), then retrieve linked PubChem Compound mixtures/components.
In this script, an additional elink search is added to find related PubChem Mixture/Component compounds via Entrez link pccompound_pccompound_mixture.
user@computer:~$ esearch -email name@xx.edu -db pubmed -query "29407984"[PMID] | \
> elink -target pccompound -name pubmed_pccompound | \
> elink -target pccompound -name pccompound_pccompound_mixture | \
> efetch -format docsum | xtract -pattern DocumentSummary -element IsomericSmiles CID InChIKey
...
...
C1CC1N2C=C(C(=O)C3=CC(=C(C=C32)N4CCNCC4)F)C(=O)O.C(CO)N(CCO)CCO 154963193 NGBBVVPJSFAHHI-UHFFFAOYSA-N
C1CC1N2C=C(C(=O)C3=CC(=C(C=C32)N4CCNCC4)F)C(=O)O.C(=O)(C(=O)O)O.[Na] 154963186 HNZYVRRDOWOQIT-UHFFFAOYSA-N
CNC.C1CC1N2C=C(C(=O)C3=CC(=C(C=C32)N4CCNCC4)F)C(=O)O 154963184 NBGZCMHVBXSHSN-UHFFFAOYSA-N
C1CC1N2C=C(C(=O)C3=CC(=C(C=C32)N4CCNCC4)F)C(=O)[OH2+] 153275427 MYSWGUAQZAJSOK-UHFFFAOYSA-O
C1CC1N2C=C(C(=O)C3=CC(=C(C=C32)N4CCNCC4)F)C(=O)[O-] 152748405 MYSWGUAQZAJSOK-UHFFFAOYSA-M
...
...tested on 2021.01.26, EDirect 14.4, total count was 375.
Description: Search PubMed with a text query, then retrieve linked PubChem Compounds.
We can also perform text queries in PubMed and retrieve linked PubChem Compounds. Note that in the below script we searched for "ionic liquids" in the [MESH] field and Imidazolium in any field. Since this query requires two pairs of quotes, we have to escape the internal quotes in order for the query to be interpreted correctly. The Entrez link pubmed_pccompound was used to find related PubChem compounds.
user@computer:~$ esearch -email name@xx.edu -db pubmed -query "\"ionic liquids\"[MESH] AND imidazolium" | \
> elink -target pccompound -name pubmed_pccompound | \
> efetch -format docsum | \
> xtract -pattern DocumentSummary -element IsomericSmiles CID InChIKey
C1=CC2=CC(=C(C(=C2C(=O)C(=C1)O)O)O)O 135403797 WDGFFVCWBZVLCE-UHFFFAOYSA-N
C1=NC2=C(N1[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N=C(NC2=O)N 135398635 NYHBQMYGNKIUIF-UUOKFMHZSA-N
CCCCCCCCN1C=C[N+](=C1C2=[N+](C=CN2CCCC)C)C 123995430 DRJFJBHYMOHPHX-UHFFFAOYSA-N
CC(=O)OC1=[N+](C=CN1CC=C)C 123614562 XSXMFLUARQMOLS-UHFFFAOYSA-N
C[N+]1=C(N(C=C1)CCCCCCCCCCCCS)OC(=O)OC2=[N+](C=CN2CCCCCCCCCCCCS)C 123431445 DRJOSAVMFCYCSU-UHFFFAOYSA-P
...tested on 2021.01.27, EDirect 14.4, total count was 395.
Description: Search PubMed with a text query and retrieve only linked compounds containing defined chiral atoms.
We can also perform some powerful filtering with efilter. In the below script, the [ACDC] field is the defined atom chiral count in PubChem. A range of 1 through 100 was added for this [ACDC] filter. Since it is unlikely that any of the compounds would have near 100 chiral atoms, we can be fairly confident this should capture most, if not all, cases in our search.
user@computer:~$ esearch -email name@xx.edu -db pubmed -query "\"ionic liquids\"[MESH] AND imidazolium" | \
> elink -target pccompound -name pubmed_pccompound | \
> efilter -query "1:100"[ACDC] | \
> efetch -format docsum | \
> xtract -pattern DocumentSummary -element IsomericSmiles CID InChIKey
C1=NC2=C(N1[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N=C(NC2=O)N 135398635 NYHBQMYGNKIUIF-UUOKFMHZSA-N
C([C@H](C(=O)[C@H](CO)O)O)O 54067296 WXYXERHRDKEISL-ZXZARUISSA-N
B(O)(O)OCC(=O)[C@H]([C@@H]([C@@H](CO)O)O)O 53705729 BXAZSOZNRVUIGN-UYFOZJQFSA-N
C([C@H]1[C@@H]([C@H]([C@@H]([C@@H](O1)O[C@@H]2[C@@H](O[C@H]([C@@H]([C@H]2O)O)O)CO)O)O)O)O 46936190 GUBGYTABKSRVRQ-AEDSEYDFSA-N
C1[C@H](OC2=CC(=CC(=C2C1=O)O)OC3C(C(C(C(O3)CO)O)O)O)C4=CC=C(C=C4)O 42607902 DLIKSSGEMUFQOK-CEFFZDIVSA-N
...tested on 2021.01.27, EDirect 14.4, total count was 43.
Description: Search PubMed, then find linked PubChem Compounds, PubChem Compounds via PubMed MeSH, and PubChem Compound PubMed Publisher.
As seen in the previous PubChem searches, there are several Entrez links from PubMed to PubChem Compound such as pubmed_pccompound, pubmed_pccompound_mesh, and pubmed_pccompound_publisher. We can retrieve associated compounds from all three at the same time like this:
user@computer:~$ esearch -email name@xx.edu -db pubmed -query "imidazolium AND bacteria" | \
> elink -target pccompound -name pubmed_pccompound -label compounds_01 | \
> esearch -email name@xx.edu -db pubmed -query "imidazolium AND bacteria" | \
> elink -target pccompound -name pubmed_pccompound_mesh -label compounds_02 | \
> esearch -email name@xx.edu -db pubmed -query "imidazolium AND bacteria" | \
> elink -target pccompound -name pubmed_pccompound_publisher -label compounds_03 | \
> esearch -query "(#compounds_01) OR (#compounds_02) OR (#compounds_03)" | \
> efetch -format docsum | \
> xtract -pattern DocumentSummary -element IsomericSmiles CID InChIKey
C[Si](C)(O)O[Si](C)(C)O.C[Si](CCC1=CC=CC=C1)(O)O[Si](C)(CCC2=CC=CC=C2)O 155288862 HYTMPCHVCUAIOW-UHFFFAOYSA-N
CC(C1CCC(C(O1)OC2C(CC(C(C2O)OC3C(C([C@@](CO3)(C)O)NC)O)N)N)N)NC 146157093 CEAZRRDELHUEMR-NWNXOGAHSA-N
C1=CC=C2C(=C1)C=C(N2)CC3=CC=C(C=C3)C(F)(F)F.C1=CC=C2C(=C1)C=C(N2)CC3=CC=C(C=C3)C(F)(F)F 139191468 NNXWVRXROOQQNO-UHFFFAOYSA-N
CC[C@@H]1[C@@]2([C@@H]([C@H](C(=O)[C@@H](C[C@@]([C@@H]([C@H](C(=O)[C@H](C(=O)O1)C)C)O[C@@H]3[C@@H]([C@H](C[C@H](O3)C)N(C)C)O)(C)OC)C)C)N(C(=O)O2)CCCCN4C=C(N=C4)C5=CN=CC=C5)C 138402871 LJVAJPDWBABPEJ-WMGYHEQLSA-N
CCOC(=O)/C(=N\NC1=CC=CC2=C1N=CC=C2)/C3=[N+](C=CN3)C 136199795 ZHOWQGCGVQGEKD-UHFFFAOYSA-O
...
...tested on 2021.01.27, EDirect 14.4, total count was 568.
Description: Search PubMed for an affiliation, find related PubChem Compounds, then retrieve related CIDs for each PMID.
If we want to retrieve the PMID <--> CID relationships (for Entrez link pubmed_pccompound), we can achieve this using the -cmd neighbor option in elink:
user@computer:~$ esearch -email name@xx.edu -db pubmed -query "(university of alabama[AFFL]) \
> NOT (birmingham[AFFL] OR huntsville[AFFL])" \
> -datetype PDAT -mindate 2010 -maxdate 2020 | \
> elink -target pccompound -name pubmed_pccompound -cmd neighbor | \
> xtract -pattern LinkSet -element Id
...
...
21800250
21783326 18679079 8914 942 702
21782896
21756136
21728552
21718269
21711000 561577 169577 166929 166928 164636
21702462
21693669
21692575
...
...tested on 2021.01.27, EDirect 14.4, total count was 3639 (returns all PMIDs, not all have linked CIDs).
The first column contains the PMIDs and the second column contains the linked PubChem CIDs (from the pubmed_pccompound links). As an aside, the PubMed query for "university of alabama" in the affiliation field ([AFFL]) excludes (NOT operator) any results containing huntsville or birmingham in the affiliation. This excludes references from University of Alabama at Birmingham and University of Alabama at Huntsville (including collaborative references with the Tuscaloosa campus).
Description: Search PubMed for an article, find related PubChem BioAssays, then retrieve some BioAssay data.
user@computer:~$ esearch -email name@xx.edu -db pubmed -query "32459468"[PMID] | \
> elink -target pcassay -name pubmed_pcassay | \
> efetch -format docsum | \
> xtract -pattern DocumentSummary -element AID CurrentSourceName AssayName ActiveSidCount TargetCount
1347414 National Center for Advancing Translational Sciences (NCATS) qHTS to identify inhibitors of the type 1 interferon - major histocompatibility complex class I in skeletal muscle: Secondary screen by immunofluorescence 0 1
1347412 National Center for Advancing Translational Sciences (NCATS) qHTS assay to identify inhibitors of the type 1 interferon - major histocompatibility complex class I in skeletal muscle: Counter screen cell viability and HiBit confirmation 0 1
1347415 National Center for Advancing Translational Sciences (NCATS) qHTS to identify inhibitors of the type 1 interferon - major histocompatibility complex class I in skeletal muscle: tertiary screen by RT-qPCR 34 1
1347413 National Center for Advancing Translational Sciences (NCATS) qHTS to identify inhibitors of the type 1 interferon - major histocompatibility complex class I in skeletal muscle: tertiary screen by RT-qPCR, retest select compounds 3 1
...tested on 2021.01.27, EDirect 14.4, total count was 7.
Description: Search PubMed for an article, find cited articles, then related PubChem BioAssays.
If we want to retrieve the PMID <--> AID relationships (for Entrez link pubmed_pcassay), we can achieve this using the -cmd neighbor option in elink. Note that here we queried PubMed for an article, then found the cited articles with elink -cited, before piping these results into the Entrez link pubmed_pcassay.
user@computer:~$ esearch -email name@xx.edu -db pubmed -query "17876319"[PMID] | \
> elink -cited | \
> elink -target pcassay -name pubmed_pcassay -cmd neighbor | \
> xtract -pattern LinkSet -element Id
...
...
21167154
21164511
21159777
21138309 568760 568754 568753 568763 568762 568761 568759 568758 568757 568756 568755
21131971
21129186
...
...tested on 2021.01.27, EDirect 14.4, total count was 366 (returns all PMIDs, not all have linked AIDs).
In the above table, the first column contains the PMIDs, subsequent columns contain the linked BioAssays (AIDs).
Description: Search PubChem BioAssay for assays from a specific source name and then find related PubMed literature.
In the below script, we first use esearch to query PubChem BioAssay for IUPHAR/BPS_Guide_to_PHARMACOLOGY in the Source Name field ([SNME]). This result is then piped into elink to retrieve linked records in the PubMed database (pcassay_pubmed). The efilter function was used to limit the results to the last 5 years. This resulted in 332 record, and we used efetch to retrieve the PubMed records as XML, followed by xtract to extract out some bibliographic information.
user@computer:~$ esearch -email name@xx.edu -db pcassay -query "IUPHAR/BPS_Guide_to_PHARMACOLOGY"[SNME] | \
> elink -target pubmed -name pcassay_pubmed | \
> efilter -mindate 2015 -maxdate 2020 -datetype PDAT | \
> efetch -format xml | \
> xtract -pattern PubmedArticle -element MedlineCitation/PMID -first Author/LastName \
> Author/Initials ISOAbbreviation PubDate/Year Volume Issue MedlinePgn
29722898 Fu R Br. J. Pharmacol. 2018 175 14 3034-3049
29688582 Kato M Br J Clin Pharmacol 2018 84 8 1821-1829
29683659 Pike KG J. Med. Chem. 2018 61 9 3823-3841
29674331 Kawaharada S J. Pharmacol. Exp. Ther. 2018 366 1 58-65
29672049 Gucký T J. Med. Chem. 2018 61 9 3855-3869
29620892 Nikolaou A J. Med. Chem. 2018 61 8 3697-3711
29615471 Xu X J. Pharmacol. Exp. Ther. 2018 365 3 624-635
29608575 Taylor Meadows KR PLoS ONE 2018 13 4 e0193236
...tested on 2021.01.27, EDirect 14.4, total count was 332.
Description: Search PubChem BioAssay for an assay, find related PubChem Compounds, and retrieve some property data for the compounds.
In the below script, we first use esearch to query PubChem BioAssay for the assay ID 527855 in the [UID] field. This result is then piped into elink to retrieve linked compounds in the PubChem Compound database (pcassay_pccompound). In this case, there were 16 compounds and we used efetch to retrieve the CID records as docsum XML, followed by xtract to extract the IsomericSmiles, CID, HydrogenBondDonorCount, HydrogenBondAcceptorCount, MolecularWeight, and XLogP values.
user@computer:~$ esearch -email name@xx.edu -db pcassay -query "527855"[UID] | \
> elink -target pccompound -name pcassay_pccompound | \
> efetch -format docsum | \
> xtract -pattern DocumentSummary -element IsomericSmiles CID HydrogenBondDonorCount HydrogenBondAcceptorCount \
> MolecularWeight XLogP
CN(CC1=CC=CC=C1)C(=O)C2=C(NC(=N2)C3=CC=CC=C3)C(=O)O 52949178 2 4 335.400 2.9
C1=CC=C(C=C1)CCN(CC2=CC=CC=C2)C(=O)C3=C(NC(=N3)C4=CC=CC=C4)C(=O)O 52948352 2 4 425.500 4.8
CN(CC(=O)O)C(=O)C1=C(NC(=N1)C2=CC=CC=C2)C(=O)O 52947957 3 6 303.270 1
C1=CC=C(C=C1)CNC(=O)C2=C(NC(=N2)C3=CC=CC=C3)C(=O)O 52946755 3 4 321.300 2.7
CCOC(=O)CN(CC1=CC=CC=C1)C(=O)C2=C(NC(=N2)C3=CC=CC=C3)C(=O)O 52945544 2 6 407.400 3.2
C1=CC=C(C=C1)CN(CC2=CC=CC=C2)C(=O)C3=C(NC(=N3)C4=CC(=CC=C4)Cl)C(=O)O 52944295 2 4 445.900 5
CCNC(=O)C1=C(NC(=N1)C2=CC=CC=C2)C(=O)O 52941818 3 4 259.260 1.6
CNC(=O)C1=C(NC(=N1)C2=CC=CC=C2)C(=O)O 52941817 3 4 245.230 1.2
...tested on 2021.01.27, EDirect 14.4, total count was 16.
Description: Search PubChem BioAssay for an assay, find related assays based on similar publications, then find related PubChem Compounds.
If we want to retrieve the AID <--> CID relationships (for Entrez link pcassay_pccompound), we can achieve this using the -cmd neighbor option in elink. Here we queried PubChem BioAssay for an assay, then found related assays by similar publication list using elink (pcassay_pcassay_similar_publication_list). This result was then piped into the Entrez link pcassay_pccompound.
user@computer:~$ esearch -email name@xx.edu -db pcassay -query "527855"[UID] | \
> elink -target pcassay -name pcassay_pcassay_similar_publication_list | \
> elink -target pccompound -name pcassay_pccompound -cmd neighbor | \
> xtract -pattern LinkSet -element Id
...
...
601409 54580326
601408 54580326 53257623
601154 54580326
657046 16093559
657045 70695880 70693764 70687505 70687504 70687503 70683264 70683263 70681155 70681154 70681153 60150625
527862 52948352
527861 52948352
...
...
...In the above table, the first column contains the AIDs, subsequent columns contain the linked PubChem Compounds (CIDs).
tested on 2021.01.27, EDirect 14.4, total count was 81 (returns all AIDs, not all have linked CIDs).