Table 2 Manual verification of proteins linked to positively classified publications.

From: Compilation of parasitic immunogenic proteins from 30 years of published research using machine learning and natural language processing

PubMed ID	Year	Row	Protein(s)	UniProt ID	e_Protein(s)	e_UniProt	Species	Prot
28424680	2017	2	Nucleoside triphosphate hydrolase-II^a	A0A7J6JVX4	Hydrolase, NTPase II	A0A7J6K3V0 A0A7J6JVX4	T. gondii	Yes
23928460	2013	11	Rhoptry protein 5 (ROP5)	Q3YJR4	Rhoptry protein ROP5, Type II rhoptry protein 5A, Type III rhoptry protein 5A, Type I rhoptry protein 5A	A0A125YQ30 Q3YJR4 B9QLN8 B9Q3F2	T. gondii	Yes
26421596	2014	22	Toxoplasma gondii 10 kDa excretory–secretory antigen (TgESA10)	R4H6A8	Ubiquitin	R4H6A8	T. gondii	Yes
14500491	2003	33	Merozoite surface protein 1 (MSP1)^a	P13828	Merozoite surface protein 1	Q9GSA3	P. yoelii	Yes
29599776	2018	44	Amastigote 2 (A2)^a	A4HZU7 Q26351	Stage-specific S antigen-like protein, stage-specific S antigen homolog,	A4HZU7 Q26351	L. infantum	Yes
7595214	1995	1737	Sporozoite surface protein 2 (PfSSP2)^a	Q26020	Sporozoite surface protein 2	Q26020	P. falciparum	No^b
21715579	2011	1747	Pfs230^a	P68874	Gametocyte surface protein P230	P68874	P. falciparum	Yes
9106193	1996	1757	Merozoite surface protein 1^a	P04933	Merozoite surface protein 1	Q8IJ53	P. falciparum	No^b
29524527	2017	1767		False positive			T. gondii	No
11349025	2001	1777	Paramyosin (Pmy)^a	A0A3Q0KD88	Paramyosin	A0A3Q0KD88	S. mansoni	No^b

Year = year of publication; Row = row position on sheet [Candidates per PubID] in Supplementary Table S3. This sheet contains 1776 PubMed IDs and their relative keyword counts that were classified as abstracts containing protein names considered worthy vaccine candidates for further investigation. The rows are in descending order based on the ‘Protection’ column. Rows were chosen at regular intervals from the top and bottom for manual verification; Protein(s) = protein name(s) specified in publication. Names with strikethrough are not vaccine candidates and therefore the classification is a false positive; UniProt ID. = UniProt ID(s) linked to protein name; e_Protein(s) = names automatically extracted from publication title+abstract; e_UniProt = UniProt ID(s) linked to protein names, which in effect are the representatives of the vaccine candidates listed in Supplementary Table S4. UniProt IDs underlined exactly match to the protein identifier in the publication. UniProt IDs in bold are incorrect with respect to the protein name e.g., Q9GSA3 is the ID for ‘merozoite surface protein’ and not ‘merozoite surface protein 1’; Species = the source species for the proteins; Prot. = ‘Yes’ or ‘No’ whether the publication reports testing in an animal model for protein immunogenicity.
^aNo formal identifier e.g., GenBank accession No. or UniProt ID given in publication. The UniProt ID shown is based on the protein name only.
^bProtein reported in other publications as a possible vaccine candidate.

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Table 2 Manual verification of proteins linked to positively classified publications.

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