I searched in internet and all I found was that we have to search the name of journal in "https://mjl.clarivate.com/" and if it indexed as: SCIE or SSCI or ESCI then the journal is indexed as ISI journal. but I wanted to submit my paper in "https://academic.oup.com/painmedicine" and I serached it in clarivate and it said that it is indexed as SCIE. But when I email to the editor of painmedicine journal he said that their journal is not rated or indexed as ISI. Now I am very confused that which journal is ISI?
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1Various unneeded comments were removed here (by multiple moderators); let us remember to be nice. – cag51 Jan 02 '21 at 00:40
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The approach you found - that of looking for the journal in the Master Journal List of Web of Science (WoS) - is the correct one. Pain Medicine is indeed indexed in SCIE and thus in one of WoS' databases.
Note that WoS was originally created by ISI (Institute for Scientific Information), but is now curated by Clarivate Analytics. Thus, the label of an "ISI-rated journal" is not entirely correct, and it is possible that due to this incorrect label, the person with whom you corresponded did not understand what you meant.

anpami
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Thank you so much. What are the other abbrevation like SCIE means that a paper is belong to WoS database? For example SCI or ESCI and etc – omidreza nouri Jan 02 '21 at 19:56
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SCI, SCIE, SSCI, ESCI - they all belong to Web of Science. The four abbreviations denote four different databases (or indexes) within the overarching platform WoS. See also https://academia.stackexchange.com/questions/127695/is-there-any-relation-between-them-like-esci-is-less-than-scie-and-scie-is-less?rq=1 for some details, if that helps. – anpami Jan 03 '21 at 07:04