Error: No author name specified.
\n"; $this->OutputHtml(); } $this->Author = str_replace("_", " ", $this->Author); if (isset($_GET['OrderBy'])) $this->OrderBy = $_GET['OrderBy']; if (isset($_SESSION['PostData'])) { $this->PostData = $_SESSION['PostData']; // Get the session saved data $this->OrderBy = "score"; } if (empty($this->OrderBy)) $this->OrderBy = "year"; $this->GetBasicCounts(); if (isset($this->PostData['Searches'])) $this->MakeIdLists(); $this->GetDocDetails(); $this->GetDetailsFromBmc(); if (!empty($this->FullName)) $this->GetFullNameCounts(); $this->PrintResults(); } function GetBasicCounts() { try { $eSearch = new eSearch( 'pubmed', "\"" . $this->Author . "\"", null, null, 20, 'count'); $eSearch->Run(2); $this->Counts['PubMed (all)'] = $eSearch->Count; $this->QueryKey = $eSearch->QueryKey; $this->WebEnv = $eSearch->WebEnv; $eSearch = new eSearch( 'pubmed', "\"" . $this->Author . "\" AND (free full text[sb])", null, null, 20 ); $eSearch->Run(2); $this->Counts['Open Access'] = $eSearch->Count; $this->OaIdList = $eSearch->IdList; $eSearch = new eSearch( 'pubmed', "\"" . $this->Author . "\"", null, null, 20, 'count'); $eSearch->RelDate = 3652; $eSearch->Run(2); $this->Counts['PubMed (10yr)'] = $eSearch->Count; $eSearch = new eSearch( 'pubmed', "\"" . $this->Author . "\"", null, null, 20, 'count'); $eSearch->RelDate = 1826; $eSearch->Run(2); $this->Counts['PubMed (5yr)'] = $eSearch->Count; $eSearch = new eSearch( 'pubmed', "\"" . $this->Author . "\"", null, null, 20, 'count'); $eSearch->RelDate = 365; $eSearch->Run(2); $this->Counts['PubMed (1yr)'] = $eSearch->Count; $eSearch = new eSearch( 'pmc', "\"" . $this->Author . "\"", null, null, 20, 'count'); $eSearch->Run(2); $this->Counts['PMC (all)'] = $eSearch->Count; $eSearch = new eSearch( 'pmc', "\"" . $this->Author . "\"", null, null, 20, 'count'); $eSearch->RelDate = 3652; $eSearch->Run(2); $this->Counts['PMC (10yr)'] = $eSearch->Count; $eSearch = new eSearch( 'pmc', "\"" . $this->Author . "\"", null, null, 20, 'count'); $eSearch->RelDate = 1826; $eSearch->Run(2); $this->Counts['PMC (5yr)'] = $eSearch->Count; $eSearch = new eSearch( 'pmc', "\"" . $this->Author . "\"", null, null, 20, 'count'); $eSearch->RelDate = 365; $eSearch->Run(2); $this->Counts['PMC (1yr)'] = $eSearch->Count; } catch (Exception $e) { $this->Html = "Caught an exception while trying to fetch document summaries (".$e->getMessage()."). Reloading the page to try again...
\n"; $this->OutputHtml(true); } } function MakeIdLists() { foreach ($this->PostData['Searches'] as $Search) { $SearchTerm = "\"" . $this->Author . "\" (" . $Search['SearchString'] . ")"; try { $eSearch = new eSearch( "pubmed", $SearchTerm, "1900/01/01", date('Y/m/01'), $Search['AtMost'] ); $eSearch->Run(2); } catch (Exception $e) { $this->Html .= "Warning: caught an exception when trying to retreive the XML data from PubMed. I am going to reload the page and hope that the problem goes away. The error given was: " . $e->getMessage() . "
\n"; $this->SaveReload(); exit; } if (is_array($eSearch->IdList)) $this->IdLists[$Search['SearchString']] = $eSearch->IdList; elseif (is_string($eSearch->IdList)) $this->IdLists[$Search['SearchString']][] = $eSearch->IdList; // Calculate the weight to be given to each search -- the weight diminishes logarithmically thus giving additional weight to rare terms $weight[$Search['SearchString']] = 2; if ($Search['Count'] < 1000000) $this->Weight[$Search['SearchString']] = 3; if ($Search['Count'] < 100000) $this->Weight[$Search['SearchString']] = 4; if ($Search['Count'] < 10000) $this->Weight[$Search['SearchString']] = 6; if ($Search['Count'] < 1000) $this->Weight[$Search['SearchString']] = 9; if ($Search['Count'] < 100) $this->Weight[$Search['SearchString']] = 13; $this->Counts[$Search['SearchString']] = $eSearch->Count; } } function GetDocDetails() { // Get some stats from the full publication list $eSearch = new eSearch( 'pubmed', "\"" . $this->Author . "\"", null, null, 20 ); $eSearch->Run(2); for ($eFs = 0; $eFs < $eSearch->Count; $eFs += 50) { try{ $eFetch = new eFetch( 'pubmed', $eSearch->QueryKey, $eSearch->WebEnv, $eSearch->Translation, $eFs, 50 ); $eFetch->Run(1); $eSummary = new eSummary( 'pubmed', $eSearch->QueryKey, $eSearch->WebEnv, $eFs, 50 ); $eSummary->Run(1); } catch (Exception $e) { $eSearch->DeleteCache(); $eSummary->DeleteCache(); unset($eSearch); try{ $eSearch = new eSearch( 'pubmed', "\"" . $this->Author . "\"", null, null, 20 ); $eSearch->Run(2); $eFetch = new eFetch( 'pubmed', $eSearch->QueryKey, $eSearch->WebEnv, $eSearch->Translation, $eFs, 50); $eFetch->Run(1); $eSummary = new eSummary( 'pubmed', $eSearch->QueryKey, $eSearch->WebEnv, $eFs, 50 ); $eSummary->Run(1); } catch (Exception $f) { $this->Html = "Caught an exception while trying to fetch document summaries (".$e->getMessage()."). Reloading the page to try again...
\n"; $this->OutputHtml(true); } } foreach ($eFetch->Array['PubmedArticle'] as &$Pub) { if (!empty($eSummary->Array['DocSum'][$Pub['MedlineCitation']['PMID']])) $Pub = array_merge($Pub, $eSummary->Array['DocSum'][$Pub['MedlineCitation']['PMID']]); if (empty($Pub['Source'])) { if (!empty($Pub['MedlineCitation']['Article']['Journal']['ISOAbbreviation'])) $Pub['Source'] = $Pub['MedlineCitation']['Article']['Journal']['ISOAbbreviation']; else $Pub['Source'] = $Pub['MedlineCitation']['Article']['Journal']['Title']; } if (empty($Pub['Id'])) $Pub['Id'] = $Pub['MedlineCitation']['PMID']; // Count the journals if (isset($this->Journals[$Pub['Source']])) $this->Journals[$Pub['Source']] += 1; else $this->Journals[$Pub['Source']] = 1; $Pub['Classes'][] = str_replace(" ", "_", $Pub['Source']); // Count the publishers if (isset($Pub['PubmedData']['ArticleIdList']['doi'])) { $Doi = explode("/", $Pub['PubmedData']['ArticleIdList']['doi']); if (isset($this->Dois[$Doi[0]])) $this->Dois[$Doi[0]] += 1; else $this->Dois[$Doi[0]] = 1; if ($Doi[0] == '10.1186') $this->BmcPapers[] = $Doi[1]; $Pub['Classes'][] = str_replace(".","", $Doi[0]); } // Languages if (isset($Pub['LangList']['Lang'])) { if (isset($this->Languages[$Pub['LangList']['Lang']])) $this->Languages[$Pub['LangList']['Lang']] += 1; else $this->Languages[$Pub['LangList']['Lang']] = 1; $Pub['Classes'][] = 'lang-' . $Pub['LangList']['Lang']; } // Authorship if (count($Pub['MedlineCitation']['Article']['AuthorList']) == 1) { $Pub['FirstAu'] = true; $Pub['LastAu'] = true; } else { $i = 1; foreach ($Pub['MedlineCitation']['Article']['AuthorList'] as $k => $v) { if (isset($l)) unset($l); if (($i == 1) and ($k == $this->Author)) $Pub['FirstAu'] = true; if (isset($v['Initials'])) $l = $v['LastName'] . ' ' . substr($v['Initials'], 0, 1); if (($k == $this->Author) OR (isset($l) and ($l == $this->Author))) { if (isset($v['MiddleName'])) $FullName = array($v['ForeName'], $v['MiddleName'], $v['LastName']); //elseif (isset($v['Initials']) and strlen($v['Initials']) > 1) $FullName = array($v['ForeName'], $v['LastName']); else $FullName = array((isset($v['ForeName']) ? $v['ForeName'] : $v['Initials']), $v['LastName']); $FullName = implode(" ", $FullName); if (isset($this->FullName[$FullName])) $this->FullName[$FullName] += 1; else $this->FullName[$FullName] = 1; if (isset($Pub['MedlineCitation']['Article']['Affiliation']) and (empty($this->Affiliations[$FullName]) OR !in_array($Pub['MedlineCitation']['Article']['Affiliation'], $this->Affiliations[$FullName]))) $this->Affiliations[$FullName][] = $Pub['MedlineCitation']['Article']['Affiliation']; } else { if (!empty($this->CoAuthors[$k])) $this->CoAuthors[$k] += 1; else $this->CoAuthors[$k] = 1; } $i++; } if ($k == $this->Author) $Pub['LastAu'] = true; } if (!empty($Pub['FirstAu'])) { if (!empty($this->Counts['First Author'])) $this->Counts['First Author'] += 1; else $this->Counts['First Author'] = 1; $Pub['Classes'][] = "FirstAu"; } if (!empty($Pub['LastAu'])) { if (!empty($this->Counts['Last Author'])) $this->Counts['Last Author'] += 1; else $this->Counts['Last Author'] = 1; $Pub['Classes'][] = "LastAu"; } if (isset($Pub['MedlineCitation']['Article']['Journal']['JournalIssue']['PubDate']['Year'])) { if (!empty($this->Years[$Pub['MedlineCitation']['Article']['Journal']['JournalIssue']['PubDate']['Year']])) $this->Years[$Pub['MedlineCitation']['Article']['Journal']['JournalIssue']['PubDate']['Year']] += 1; else $this->Years[$Pub['MedlineCitation']['Article']['Journal']['JournalIssue']['PubDate']['Year']] = 1; } // Email if (!empty($Pub['FirstAu']) and !empty($Pub['MedlineCitation']['Article']['Affiliation'])) { if (strpos($Pub['MedlineCitation']['Article']['Affiliation'], '@', 0)) { $email = substr($Pub['MedlineCitation']['Article']['Affiliation'], strrpos($Pub['MedlineCitation']['Article']['Affiliation'], ' ')); if (empty($this->Emails[$FullName]) OR !in_array($email, $this->Emails[$FullName])) $this->Emails[$FullName][] = $email; } } /*********** SCORES ***********/ if (!empty($Pub['FirstAu']) and !empty($this->PostData['ScoreFirstAu'])) $this->Scores[$Pub['MedlineCitation']['PMID']] = $this->PostData['ScoreFirstAu']; elseif (!empty($Pub['LastAu']) and !empty($this->PostData['ScoreLastAu'])) $this->Scores[$Pub['MedlineCitation']['PMID']] = $this->PostData['ScoreLastAu']; else $this->Scores[$Pub['MedlineCitation']['PMID']] = 1; if (!empty($this->PostData['WeightJournal']) and (in_array($Pub['MedlineCitation']['Article']['Journal']['ISOAbbreviation'], $this->PostData['ScoreJournal']) OR in_array($Pub['MedlineCitation']['Article']['Journal']['ISSN'], $this->PostData['ScoreJournal']) OR in_array($Pub['MedlineCitation']['Article']['Journal']['ISOAbbreviation'], $this->PostData['FullJournalName']))) $this->Scores[$Pub['MedlineCitation']['PMID']] = $this->Scores[$Pub['MedlineCitation']['PMID']] * $this->PostData['WeightJournal']; if (!empty($this->PostData['ScoreDoi']) and isset($Doi) and in_array($Doi[0], $this->PostData['ScoreDoi'])) $this->Scores[$$Pub['MedlineCitation']['PMID']] = $this->Scores[$Pub['MedlineCitation']['PMID']] * $this->PostData['WeightDoi']; // Weight the score by age if (isset($this->PostData['ScoreAge']) and $this->PostData['ScoreAge']) { $Timestamp = strtotime(implode("/", $Pub['MedlineCitation']['Article']['Journal']['JournalIssue']['PubDate'])); $Age = time() - $Timestamp; $Age = $Age / 31570560; if ($Age < 1) $Weight = 2; // If the publication is less than a year old, double the score else $Weight = 0.5 + (1 / $Age); // Otherwise, weight it by 0.5 + (1 / Age) $this->Scores[$Pub['MedlineCitation']['PMID']] = $this->Scores[$Pub['MedlineCitation']['PMID']] * $Weight; } // Weight the score by search matches if (!empty($this->IdLists)) { foreach ($this->IdLists as $String => $IdList) { if (in_array($Pub['MedlineCitation']['PMID'], $IdList)) { $this->Scores[$Pub['MedlineCitation']['PMID']] = $this->Scores[$Pub['MedlineCitation']['PMID']] * $this->Weight[$String]; $Pub['Classes'][] = str_replace(" ", "_", $String); } } } $this->Publications[$Pub['MedlineCitation']['PMID']] = $Pub; } } } function GetDetailsFromBmc() { // Try to find author details by looking on BioMed Central if (!empty($this->Dois['10.1186'])) { foreach ($this->BmcPapers as $Doi) { $Bmc = new BioMedCentral( "10.1186/" . $Doi ); $Bmc->GetXmlFile(); if (isset($Bmc->Error)) continue; $Bmc->XmlToArray(); if (isset($Bmc->Array['fm']['bibl']['aug'][$this->Author])) { if (!empty($Bmc->Array['fm']['bibl']['aug'][$this->Author]['mi'])) $FullName = array($Bmc->Array['fm']['bibl']['aug'][$this->Author]['fnm'], $Bmc->Array['fm']['bibl']['aug'][$this->Author]['mi'], $Bmc->Array['fm']['bibl']['aug'][$this->Author]['snm']); else $FullName = array($Bmc->Array['fm']['bibl']['aug'][$this->Author]['fnm'], $Bmc->Array['fm']['bibl']['aug'][$this->Author]['snm']); $FullName = implode(" ", $FullName); if (isset($this->FullName[$FullName])) $this->FullName[$FullName] += 1; else $this->FullName[$FullName] = 1; if (!empty($Bmc->Array['fm']['bibl']['aug'][$this->Author]['email']) and (empty($this->Emails[$FullName]) OR !in_array($Bmc->Array['fm']['bibl']['aug'][$this->Author]['email'], $this->Emails[$FullName]))) $this->Emails[$FullName][] = $Bmc->Array['fm']['bibl']['aug'][$this->Author]['email']; if (!empty($Bmc->Array['fm']['bibl']['aug'][$this->Author]['insr'])) { if (isset($Bmc->Array['fm']['bibl']['aug'][$this->Author]['insr']['iid'])) { if (is_array($Bmc->Array['fm']['bibl']['aug'][$this->Author]['insr']['iid'])) { foreach ($Bmc->Array['fm']['bibl']['aug'][$this->Author]['insr']['iid'] as $v) { $AffiliationId = $v; if (!empty($Bmc->Array['fm']['bibl']['insg']['ins'][$AffiliationId])) $Affiliation = $Bmc->Array['fm']['bibl']['insg']['ins'][$AffiliationId]; if (empty($this->Affiliations[$FullName]) OR !in_array($Affiliation, $this->Affiliations[$FullName])) $this->Affiliations[$FullName][] = $Affiliation; } } else { $AffiliationId = $Bmc->Array['fm']['bibl']['aug'][$this->Author]['insr']['iid']; if (!empty($Bmc->Array['fm']['bibl']['insg']['ins'][$AffiliationId])) $Affiliation = $Bmc->Array['fm']['bibl']['insg']['ins'][$AffiliationId]; if (empty($this->Affiliations[$FullName]) OR !in_array($Affiliation, $this->Affiliations[$FullName])) $this->Affiliations[$FullName][] = $Affiliation; } } } } } } } function GetFullNameCounts() { // Full name counts foreach ($this->FullName as $FullName => $Count) { $eSearch = new eSearch( 'pubmed', "\"" . $FullName . "\"", null, null, 20 ); $eSearch->Run(2); if (!empty($eSearch->Count)) { $this->Counts[$FullName] = $eSearch->Count; foreach ($eSearch->IdList as $Id) { $this->Publications[$Id]['Classes'][] = str_replace(" ", "_", $FullName); } } } } function PrintResults() { // Make the Html $this->Html = "";
$this->Html .= "
| None found. |
| Publication list (order by: date | score) |
|---|
|
Date: " . implode("-", $Pub['MedlineCitation']['Article']['Journal']['JournalIssue']['PubDate']) . " " . $Title . " " . $AuList . " " . ((!empty($this->OaIdList) and in_array($Pmid, $this->OaIdList)) ? " |
| Publication list (order by: date | score) |
|---|
| Publications[$Pmid]['Classes']) . "\" style=\"border: 1px solid #ddd;\">
Score: " . round($Score, 2) . " " . $Title . " " . $AuList . " " . ((!empty($this->OaIdList) and in_array($Pmid, $this->OaIdList)) ? " |
| Search counts | \n"; $SearchLinks = array( "PubMed (all)" => "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22" . $this->Author . "%22", "Open Access" => "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22" . $this->Author . "%22 AND (free full text[sb])", "PubMed (10yr)" => "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22" . $this->Author . "%22 AND ("last 10 years"[PDat])", "PubMed (5yr)" => "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22" . $this->Author . "%22 AND ("last 5 years"[PDat]", "PubMed (1yr)" => "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22" . $this->Author . "%22 AND ("last 1 years"[PDat]", "PMC (all)" => "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pmc&Cmd=Search&Term=%22" . $this->Author . "%22", "PMC (10yr)" => "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pmc&Cmd=Search&Term=%22" . $this->Author . "%22 AND ("last 10 years"[PDat]", "PMC (5yr)" => "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pmc&Cmd=Search&Term=%22" . $this->Author . "%22 AND ("last 5 years"[PDat]", "PMC (1yr)" => "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pmc&Cmd=Search&Term=%22" . $this->Author . "%22 AND ("last 1 years"[PDat]", "First Author" => "javascript:highLight('FirstAu')", "Last Author" => "javascript:highLight('LastAu')", ); foreach ($this->Counts as $k => $v) { $this->Html .= "|
|---|---|
| " . ((strlen($k) > 26) ? substr($k, 0, 23) . '...' : $k) . " | " . (isset($SearchLinks[$k]) ? "" . $v . "" : "" . $v . "") . " |
| Languages | \n"; arsort($this->Languages); $i = 0; foreach ($this->Languages as $k => $v) { $this->Html .= "|
|---|---|
| " . $k . " | " . $v . " |
| Favourite journals | \n"; arsort($this->Journals); $i = 0; foreach ($this->Journals as $k => $v) { $this->Html .= "|
|---|---|
| " . $k . " | Author . "%22 AND ("" . $k . ""[TA])\">" . $v . " |
| Favourite publishers | \n"; arsort($this->Dois); $i = 0; foreach ($this->Dois as $k => $v) { $this->Html .= "|
|---|---|
| " . (isset($PublisherTranslation[$k]) ? $PublisherTranslation[$k] : $k) . " | ". $v . " |
| Co-authors | \n"; arsort($this->CoAuthors); $i = 0; foreach ($this->CoAuthors as $k => $v) { $this->Html .= "|
|---|---|
| " . $k . " | ". $v . " |
| History | \n"; $h = 0; for ($y = date('Y'); !empty($this->Years); $y--) { if (empty($this->Years[$y])) { $Years[$y] = 0; continue; } if ($this->Years[$y] > $h) $h = $this->Years[$y]; $Years[$y] = $this->Years[$y]; unset($this->Years[$y]); } $i = 0; foreach ($Years as $y => $c) { $width = (135 / $h) * $c; $this->Html .= "|
|---|---|
| " . $y . " | " . (!empty($c) ? $c : " ") . " |
... time elapsed: $Time seconds.
Content from pubmed used under NLM terms of use (NLM disclaimer). Content from BioMed Central and the Open-Access padlock (PLoS) used under the terms of the Creative Commons Attribution license.
![\"[Open](\"images/padlock.gif\" "\\"Free")
" : "") . "" . $Pub['Source'] . " " . (isset($Pub['SO']) ? $Pub['SO'] : implode("-", $Pub['MedlineCitation']['Article']['Journal']['JournalIssue']['PubDate'])) . "
" . (isset($Pub['PubmedData']['ArticleIdList']['doi']) ? "